Partly jossed. She creates duplicates of them using hair samples, their pictures, and her magic, and has them act as badly as they can in order to throw the real six off balance.
Also the series has had a few more expanded universe callbacks, so why not mirror mirror?
Jossed - see above.
What it is is anyone's guess(though am I the only one that hopes it isn't Chrysalis pulling a Heel–Face Turn?), but when "Crusaders of the Lost Mark" aired, also midway through the season, people kept saying that something like that would have been more anticipated in a season or even series finale. For something as anticipated as Queen Chrysalis's return to happen midway through the season instead of the season finale, there's probably gonna be a massive change to somepony as a consequence.
Jossed. Her plan falls apart and she slips away, swearing to get her revenge later.
Remember Fluttershy's theory about the Elements not having to vanish at the end of last season because they were used to heal, instead of something more negative? The Elements have never been used to effectively kill any living being before (even if they were technically wood given that life through magic), so if the process of banishing the Pony of Shadows to Limbo could have made them vanish for good... what would having them turn dark and destroy the Mean 6 do to them? We know that they didn't actually vanish.
Even the process of having them turn dark could mean bad things, even if the killing had no effect on them. They're VERY powerful magical artifacts after all.
Hell, this could even factor into Chrysalis' next plan. Turn them briefly dark enough, and they might stick that way. And if they're the thing keeping balance in this world that could be very bad.
- Sometime after the events of the episode, a group of Timberwolves will find the logs that once were the Mean Six, and will use them to construct their bodies. These logs, however, will their essences or souls within them. As a result, the Mean Six possess the Timberwolves and use their new bodies to cause trouble in Ponyville. Over time, they will draw upon the magic of the Everfree Forest itself, which then restores their original bodies.
- Following a team-up between Grogar, Chrysalis, and several other villains, Grogar will have heard about what Chrysalis tried to do. Finding the logs, Grogar will use his dark magic to resurrect the Mean Six. Afterwards, he provides them with a boost in power similar to that which Megatron received when Unicron reformatted him. Furthermore, the boost in power will also see them be given their own names and new appearances to go with them. In exchange for this upgrade, the Mean Six pledge their loyalty to Grogar, perhaps serving as his Lieutenants or Enforcers.