Allen will be anti-munity/neutral, depending on how things go down. He isn't overly fond of the Initiative or what they've done, but he's not going to be supportive of the mutineers at all, either, and he wouldn't be convinced the base is better off in their hands. He can still sympathize with their frustrations and their goals, but not with their methods (or timing!!), and there are SO FEW members of the Initiative... nothing about this will sit well with him. He's of the opinion that sowing conflict now is a Bad Idea, we're all trapped on the moon.

He'll try to intervene if he sees any serious violence from either side/attempt to reason with people/help where he can, but otherwise, shounen's probably not gonna get heavily involved in any conflict.