Thain? He seems mostly an arrogant, self-important blow-hard. Not really villainous.
Allison is a tough one. She's a zealot, that's for sure. Ambitious and opportunistic. And 100% Teflon-coated. In some sense you could call her a villain. The perspective from which the story is written will really determine if she's a hero or villain. She's manipulative and ruthless. Willing to let a lot of people die to get to where she thinks things need to be. An "ends justify the means" person, for sure. But her end goal is not an evil one.
Allison? Constantly trying to get the theocracies against D'Hara in some form or another. Clearly a villain.
