I don't buy for a second that Banner would willingly sign the accords. He doesn't want to be 'controlled', he wants to not be the Hulk at all. And, especially knowing that Ross would be in charge, he most certainly would not want the government to be controlling him, telling him when to suit up and who to take out. I'd give it about six months before they started trying to use him as an unbeatable weapon against regular enemies. Of course, by that same token his most logical option would still simply be 'neither of the above'. But he would probably be willing to help Cap if he knew that his friends were in serious danger. Certainly more willing than he would be to sign up for govt. service.
Thor is a much less clear question. Obviously, if they were to appear, he would have to be opposite the Hulk, or there would be no movie. But the most logical place for him to be, I agree, is mostly neutral and kind of smug and arrogant towards the govt. His sympathies probably lie more with Cap than Stark, but being so much of an outsider to this world and culture, he would probably be most concerned with stopping the escalation.
Edit: Thinking about it a little more, I think the most logical way to write Banner in would've been as a 'neutral' prisoner - he refuses to sign the accords, but is willing to let the govt. lock him up in a comfy/high security area in hopes of keeping the hulk in check. This would make even more sense, considering he's probably still wanted for the South Africa rampage. Then Thor could've spent the first half of the movie trying to be neutral and stop the escalation, until the Hulk inevitably winds up on the loose, is massively confused by all of his friends fighting each other and Thor has to abandon his efforts to go put the green genie back in the bottle.