I think Millar has done a wonderful job of explaining the grey area. It's something that is lacking from comics a great deal, and in the world in general, that seems to be becoming increasingly polarised into the falsehoods of good and evil.
I mean, hey, Hank Pym is a wife beater, and we like the guy. Banner killed hundreds, and we have massive sympathy for him. Tony Stark is a womanising alcoholic, and frankly, we'd all love to be him.
Good and evil doesn't exist in Millar's world, as it doesn't in the real world. Which is why these books are such a hit. Hell, the whole skrull thing can be seen as a parody even, I'm sure one the characters says "things don't get more black and white than this". And it's true, they don't, ever, they don't even come close.