Mark Millar and Tom Brevoort both flatly stated that "Civil War proved Tony Stark right." There is no room for debate on this subject. Both the writer and the editor of the event have made it clear, to the point of openly insulting those who disagree with them, that the pro-reg side was morally justified in everything that it did, and that it deserved to win.
And actually, in spite of his liberal pretensions, I DO think Millar is a conservative, because in his worldview, the only way to win a fight is by being more evil than your opponents. Yes, the pro-reg side did evil things, but Millar doesn't just support them in SPITE of those things - he supports them BECAUSE of those things, just like the fans of Jack Bauer in 24 love his character BECAUSE he uses torture, because much like Dick Cheney, Millar believes that brutality should be one's FIRST resort in a fight.