So this is which would you like most, not which do you think is most likely. I'd say what's most likely is that she returns either intending to take them down from the inside or just because she can't learn to function outside of the Dollhouse. Another possibility is them bringing her back by force, she knows too much for them to let her spend too long free.

If it was up to me I'd love her to be the season 2 villain. It's a different take on the whole being attacked by a broken doll thing they had in season 1. It would also force them to face up to what they are doing to the fake imprinted personalities. Whenever the staff do seem to focus on the morality of the situation they only seem to think about the original people, never the people they create then destroy. Claire as a villain would be a great way to force them to face it. Of course to make it line up with epitaph one they would have to end doing something like wiping her and re-imprinting her with a calmer version of Claire or something, but I think that would be cool too. It's a scary look at them taking people and removing what makes them human to make them more docile or useful, which seems to fit with the overall theme of the show.

Hmm... I really don't know! I mean if they're going to cancel the show (and let's be realistic, if a few millions won't start watching it right now, they will cancel) it would be totally pointless to make her a villain for 2 episodes, or anything else for that matter. And that's a real shame, because I love Dollhouse and I was kinda hoping for some Claire/Topher action, so let's hope they won't ruin our precious show by cutting it after just 2 seasons! I'd hate to see Firefly all over again. I get depressed easily ;)

Edit: I forgot to write my final answer! ;P I would love to see her as a villain but (hopefully) in season 3

Edit no.2: Okay, I'm boring ;P If there isn't going to be third season I would like her to return and work for the Dollhouse like she did before.

Yeah I don't want to see her become a villian because I just think she is too nice. The putting mice in boxes and scaring Topher was like her limit I think =P I think its most likely she will try to bring down the Dollhouse but what I want is for her to get her original personality back.
Also, having her & Alexis together on screen again would be too difficult. I would literally have to bite my tongue soI didn't scream "FREEEEDDDDD, WHY DID YOU HAVE TO DIE? YOU TWO WERE PERFECT!!"

Whiskey said she didn't want her real personality back. If she got it back then Whiskey/Claire wouldn't exist anymore and she didn't want to die.