Dude, you still gotta admit that right or wrong, Tony and Reed are acting crazy as all hell. Removing habeus corpus is bad enough, but creating a superhero team headed up by Norman Osborn and consisting of members like Bullseye and Venom? Yeah, that's smart. That's not at all a problem you're going to have to deal with another time when they inevitably go rogue. I mean, come on. Norman Freakin' Osborn. Then you've got the idea that somehow, cloning Thor is a great idea, because clones have always worked out well in the past. Then he kills someone, and its "Oh well, some kids died and their mom gave me one of their toys so it doesn't really matter how many people I kill or imprison."
I agree with you though, that Millar doesn't know what he's doing. Cap is acting idiotic in all of the official titles. I just like it when one of the side guys, like JMS here or Peter David, do their best to make the whole stupid story make sense.
I leave you with this thought:
""Each man must for himself alone decide what is right and what is wrong, which course is patriotic and which isn't. You cannot shirk this and be a man. To decide against your conviction is to be an unqualified and excusable traitor, both to yourself and to your country, let me label you as they may." - Mark Twain