The growing Knight Templarism of the Jedi Order and gradual darkening of the EU is allowing for a plausible segueing into the Legacy comic series, where the Empire are the good guys.
Possible but problematic since the Order under Kol Skywalker is generally treated as a positive organization before the Ossus Project is sabotaged.
At first, one might wonder why no one considered imprisoning the infected Jedi with ysalmiri, instead of freezing them in carbonite. However, were they to do that, the secret of how to contain Jedi powers would go public, and every two-bit crime lord and gangster would be heading to Myrkr to pick up their own.
Kenth's breakdown makes total sense when you realize that it happened because he was completely Wrong Genre Savvy. Having been a former colonel in the New Republic Defense Forces, it's implied he still thinks of himself as being a soldier, or at least a former soldier. In an equivalent military setting, if the commander in chief were temporarily unavailable, another officer would take their place, with all the appropriate trappings of rank. To ensure the chain of command, lesser-ranked soldiers obey their orders and treat the temporary leader with deference. It would not be as much of a big deal for a commander-in-chief to make an under-the-table deal with another allied power (like Kenth did with Bwua'tu) and not inform their subordinates, and they would be almost expected to emphasize their new rank to ensure obedience. Unfortunately, Kenth never realized the individualistic nature of the Jedi means that they don't instinctively obey orders. The position of Grand Master is as much honorary as it is authoritative, and the Council is a democracy, not an autocracy (witness how Yoda didn't want to train Anakin in The Phantom Menace but was overruled, for example). Had Kenth understood this, the whole situation would never have happened.
While Kenth does eventually come to realize some of this, he still insists on keeping secret his deal with Bwua'tu, which even he realizes makes it seem that he doesn't/can't trust the Council members. And, just as importantly, has the authority to do this without their approval. This is what ultimately breaks their trust in him badly enough that they're willing to make the launch without his approval.
Extra Fridge Brilliance sets in when you realize that this was exactly why he was chosen in the first place. Daala would have never accepted an interim Master like Kyp, Corran, Octa, or Kyle, all of whom, to one extent or another, embody the attitude of Screw the Rules, I'm Doing What's Right!. Kam and Tionne are busy on Ossus, while Clighal has a lot on her plate in dealing with the infected Jedi. This leaves either Saba or Kenth, and as a former Imperial, Daala is no doubt more comfortable with a human man, as well as one with a military mindset.
It's not dwelt on, but if Anakin had accepted the Father's offer to become the new personification of Balance during the Clone Wars, he and/or the Son and Daughter could've killed Abeloth or kept her imprisoned. Which means that, essentially, all the events of this series are Anakin's fault. Nice Job Breaking It, Hero, indeed!
The amount of narrative attention paid to Vestara and the Sith in Omen and Abyss can feel a little redundant to readers. But it makes sense later: Not only do they serve to set up Vestara and Abeloth for the readers, but they also show just how ridiculously prevalent Chronic Backstabbing Disorder is amongst the Sith, which in turn fuels Vestara's Heel–Face Turn.
The Jedi being so willing to accept Vestara: Practically every major Jedi character in the last few decades/series has at least struggled with, if not gone over to, or started out on, the Dark Side. Given that, it makes sense that they'd be willing to welcome a Sith defector once Luke confirmed that she was genuine.
