I've been watching the argument each time it flares up, and never actually gotten around to committing my opinions to writing.
Spoiler:I hate the Cult of the Center, I really do, but in this case I can't see any reason to get worked up over thinking either character was fully in the right.
Since Season 1, we've been shown time and again that Kenny comes from a very traditionally Southern mindset as regards the arrangement of family. He comes from a tradition, of which I myself am intimately aware, that says that the mother is the caretaker and the father is the provider and defender. He measures his own worth in terms of keeping his family safe and provided for. Season 1 saw his direct family starve and die the whole way through. The circumstances were entirely out of his control (say what you will about his individual decisions, nobody is ever going to keep people comfortably fed and safe during the zombie apocalypse), but you could say that he failed in his duty as a patriarch, continually. In Season 2, he's still trying to be a good patriarch to his new, adoptive family, and still "failing", because there's simply no way to achieve the goal he's after. Every failure chips away at his sanity, and as he continually degrades, he gets worse and worse at meeting the standards he's set for himself. I'm not even going to try to argue that he wasn't a violent psychopath, but I understand why he got the way he was, and I don't particularly blame him for it.
Jane, on the other hand... I hate to phrase it this way, but the whole "this season was about loyalty, if you side with the backstabbing bitch you get the shitty ending" gives me this creepy GG vibe. Her arc was pretty clearly spelled out that she's scared of forming attachments because this is The Walking Dead, and the odds are really good that everyone you love is going to die because fuck you, happily ever after doesn't exist here. She tries hard to turn Clem to her own way of thinking, but (I guess this might be biased by my experiences) ultimately exactly the opposite happens. She starts to see how she can't just survive on her own all the time and she is going to have to form some attachments at some point. That doesn't mean she's completely turned around by the end of the story, and she's fighting her own flighty instincts all the time. Even the cliffhanger asks the question of whether she'll be able to trust the next new group of outsiders. But the idea that she's just waiting for an opportunity to kill you and take your stuff because she's Chaotic Evil, well... I don't see it.
The writing was, to put it diplomatically, not the best in Season 2. But I take issue with the idea that there was a clear hero and a clear villain in that final decision; it was a clash of two deeply flawed individuals failing to meet their own standards, embarked at the worst possible time for all involved. That's The Walking Dead for you.
You know, I would completely agree with you except,Spoiler:I feel that when she lies to Kenny about the baby being dead is when she crosses over the line from flawed character to actively screwing with people.