Jane's true intentions.
The moment Jane joins the group, she was analyzing the state of the group and who could become a problem. She didn't plan to get attached to Clementine. but she did because she reminded her of her little sister that she couldn't save. Her reasoning for leaving the group the first time was because she knew that Kenny was a ticking time bomb, she knew there was no way that Clementine would leave him, so she left. She didn't want to be there when he snaps, and gets everyone killed, she didn't want to see Clementine die, so she just avoided the who scenario by leaving. Only reason why she came back was because she felt compelled that it was her duty to save Clementine from Kenny, to show her what he's really becoming. That's why she always trying to point out every little detail to Clementine about his stability, but never once did she make false accusations about him, without realizing his state, unlike Kenny where he just throws accusations after another without even knowing a thing about her. She never gave him a chance to know anything about her, she's a closed book, but Kenny is an open book and everyone knows what he is.
Jane was willing to risk her own life to save Clementine from him. Which pretty much negates Kenny's claim after the ending where you do let Kenny kill her where he said that she only cares about herself and when he said that "once AJ dies, what's the point of living after that?" "That's something Jane will never understand." Which she did, otherwise she wouldn't had came back in the group knowing what was going to happen. Also when Kenny said that she could have stopped the fight anytime by telling him that AJ is fine and it was all a hoax. NO WAY in hell he was going to believe a thing she says, Jane knows that, that's why even at the very end if you so let her die, she kept her dignity.
Kenny is a good guy, he's still is, he shows it at the ending at Wellington where he chooses to stay behind and let the kids in. He know's that he's unstable and unfit to protect them, that's why he tells you in the ending "I don't trust myself to protect you guys, not anymore", and at the ending where you shoot him and he tells you that "you made the right choice." He knows becoming a monster, but his pride refuses to let him admit it.
Jane is a good person, she has a difficult time trusting people, which is something you can't blame her for. In an zombie apocalyptic world like this, where people survived for this long, they couldn't had survived without killing at least one person. She's a realism and she knows how to adapt to that world, and doesn't let her emotions dictate her decisions.
People may argue that going to Wellington and leaving Kenny behind was the best choice, but people have to realize if Wellington is the goal to Clementine's destination, the story line in season 3 has to intertwine to sink the story sooner or later, so no matter where you choose, the verdict in season 3 will always be the same.