Mr Fantastic isn't a Nazi, he's just a genius who is too smart fr his own good. He completely disregards personal emotion and subjective opinions if the numbers are right. If Fantastic's statistics showed that rebelling would have been the better option, he would have been more than happy to follow suit.
And for the record, Civil War was awesome.
I know nothing of comics, but I'm inclined to believe Pancake's opinion on just about anything over Talon's.