The Adam and Eve parallels involving Jim and Aurora are clear enough, especially if you compare the state of the ship everyone woke up to to the Garden of Eden. However, the story of the Garden of Eden includes 4 characters, all of which are present: the (seemingly?) benign, soft-spoken stranger whose casual comments steer the humans towards conflict and disaster—Arthur is the Serpent! And then, the wise, elderly figure who teaches lessons and provides truly helpful guidance, but remains hands-off throughout: Gus is the voice of God.
This parallel grows even deeper with the scene where Gus asks who has planted the tree, calling to mind the scene where God asks why Adam and Eve ate from the Tree of Knowledge. Also, the tree is planted in the center of the ship, much like how the Tree of Knowledge was planted in the center of the Garden.
Why does Arthur spill the beans on Jim waking Aurora even though he had specifically asked him not to? Because just before, when Jim is asked if he has any secrets, he tells Arthur that he doesn't. Effectively cancelling out his earlier instruction to the Android.
What if Jim and Gus's pods opening up wasn't exactly a malfunction? It seems awfully convenient that out of the thousands of pods on the ship, the one's that just happen to open up randomly are a skilled technician/repairman, and the captain of the ship. Maybe there was some kind of fail safe built into the AI of the ship to where any critical malfunctions would open up the pods of someone who could fix it. The passengers have to give detailed descriptions on who they are so maybe the ship knew Jim was a great mechanic which is why it woke him up when it sensed malfunctions. Same for the the captain.
Or course that begs the question why the ship didn't wake up a mechanic who was a member of the crew, who would both know more about the ship and have the authority to get everywhere needed to fix it.
Actually, Gus was not the captain of the Avalon. He was only a Deck Chief; not as important, but with enough authority to access the crews' privileges. So the ship may not have had chosen to awake those particular people.
It was mentioned in the story that the ship's computer recognised there was a problem which needed a human to fix it, but categorised said problem as not severe enough to warrant waking the Captain or any of the ship's own repair crew. It was however able to wake up a non-crewman who happened to be a skilled mechanic/engineer who could attempt to fix it. As time went on and the conditions on-board ship continued to deteriorate, the ship's computer was able to justify waking someone with actual access to most parts of the ship - aka the Deck Chief, Gus. However it still did not deem the situation severe enough to bring the Captain or the repair crew out of hibernation! This all means that the ship was effectively finding a way around its own programming in order to do its job of keeping the ship running normally - a Zeroth Law Rebellion
Optimistically, if they time it just right, their children could've lived long enough to make it to Homestead II. From their appearance, we could assume that Jim and Aurora are both in their early thirties at most, so they have a long time to have children. Of course, by the time the rest of the crew wake up, Jim and Aurora would've been long dead and their children, most likely about to become elders themselves as well, would've been left alone on the starship, but at least they have a chance to make it to the new world.
They have the autodoc. If they have one kid, they can let 'em grow up, then put 'em in stasis so they can wake up with the rest of the crew. The kid would never see their parents again, but they would get to join society.
The Artistic License – Physics article on the main page implies an even more horrifying explanation: radiation poisoning made one or both of them infertile.
Gus turned out to have suffered fatal damage from his pod's malfunction. How many other people on the Avalon might have succumbed to similar internal damage for faulty pods, and either awoke only to face a certain death, or expired during hibernation without ever regaining consciousness?
If Jim had just waited another year, he could have made it to Homestead II. If he and Gus worked fast enough to fix the reactor, he could have used Gus's Auto-Doc override to go into stasis afterward.
The horror to this horror is that, if Jim had waited another year, he would probably have lost his mind and gone through with his plan for suicide. Failing that, he may very well have never met Gus at all. Waking Aurora led to the chain of events where he planted the tree, which is why Gus made a shipwide announcement. Without the tree, he wouldn't have called out to whoever planted it. Since Gus died within a day or so of being awoken, it's entirely possible that they would never have met each other. It's also possible that Gus would have died in the command ring while trying to fix the ship, and if that happened, then Gus's band wouldn't have help Jim much. It would open doors, but he wouldn't know what to look for or where, he wouldn't have known how the diagnostics worked and in the end the repair required two people so he wouldn't have been able to repair the damage before the reactor failed. Lastly, there's nothing indicating that someone could get into the Auto Doc and still have the ability to activate the suspend feature, which was on a touch screen outside the device.
On the other hand, if Jim had died a year sooner, then the ship may have woken up Gus immediately due to its first attempt to enlist human assistance (see above) having failed. In which case, Gus might've avoided most, if not all, of the harm caused by his pod's failure due to having been released before its glitches got too severe. If nothing else, he might've had time to wake up some other crew whose pods weren't malfunctioning, and who could take over doing the repairs even if Gus himself still expired.
In-universe, as the entire plot is mostly a result of hubris on the part of the Avalon's designers.
A passenger wakes up 90 years ahead of schedule due to his pod malfunctioning. None of the AI interfaces are programmed to process the simple equation that 120 years have not passed because they are programmed to believe the stasis pod technology is foolproof. Thus they are completely useless in aiding Jim and cannot stop him waking other passengers up. Which we later learn is actually very dangerous.
Stasis pods have no means of being restarted if they wake someone up early. We later learn that there actually is a method of effectively putting someone into stasis via medical equipment. This might be too expensive to build into every single pod but surely this might be a handy feature for vital crew. Regardless there is inexplicably only one medical pod for a ship of 5,000. Even a handful of these spares the protagonists dying with only each other for company.
In the event of catastrophic ship damage which triggers the pod malfunctions that wake two passengers ahead of schedule, why isn't it standard procedure to wake a member of the crew early? That person has the authority to access the ships data to properly assess the problem, then use the medical pod to return to stasis. By the time a crewman is awakened by sheer luck, the situation has been allowed to deteriorate for 2 years, with the ship dealing with the symptoms rather than the cause and every life on the ship is in mortal danger.
Androids are affordable and common place enough that the Avalon can have one as a bartender. Surely having a few maintenance or medical androids on stand-by wouldn't be so outlandish? You'd think if there were automated cleaning bots running on the ship for 120 years, they could have a few robot mechanics check the ship periodically.
Aurora's plan was to return from Homestead II after a year. The ship lacked any machines for inducing hibernation, and information on how to build any. And sending/receiving data from earth takes decades. How is anyone supposed to go back in one year?! Also, wouldn't there be better uses for a space-worthy vessel than returning people immediately a year after?
Round trips are evidently a thing. Gus’s throwaway line about how he always feels hungover upon waking up from cryostasis strongly suggests that he’s made multiple interstellar voyages. Of course, said round trip will take 241 years, so everyone she’s ever known back on Earth—and their grandchildren—will be long dead by the time she gets back.
No reason why Homestead can't send construction robots to build a re-hibernation station in orbit around each colony world, long before it sends any humans there. That's probably how they identify and assess planets suitable for colonization in the first place: with robots.
Also, sort of tied to the above, Aurora starts her arc as a rather hubristic person:
Her plan was to make a round trip that would take over two hundred years - and then just return to her life? Girl, you're a writer, have you never read Return from the Stars? Have you never even attempted to imagine things may change? And not necessarily in the direction you'd like?
She reacts with anger when learning she won't have that. Anger. Not sadness, not fear (she does panic a bit, but she's mostly angry). The "that's not fair" emotion. Of course, Jim waking her up is not fair of him, but she doesn't know that at the moment. And it's all about her! Her plans, her "interview" with Jim, her life that he "took away". He didn't give her a chance to have a unique experience, he wasn't mad from the isolation enough to act immorally, he obviously can't be sorry for hurting her (and it sooo wasn't a side effect of his own attempt to save himself) - because he's done something she's unhappy with - that's how she treats this. You don't get the life you want, you get the life you get. As Aurora herself admits in the end:
You can't get so hung up on where you'd rather be that you forget to make the most of where you are.
To sum it up, yes, Jim did the wrong thing, but Aurora forgiving him doesn't seem, to me, Stockholm syndrome - just maturing.
