The Curmudgeonly perspective -- it's all a scam!
I'm a cynic at heart, but that's a useful perspective when viewing Hollywood machinations. Here's my take on this "controversy".
The nudity in Closer was a marketing ploy from the beginning. They hyped Natalie Portman's FIRST NUDE SCENE to get free advertising for the film. And then deciding to "protect her image" got them more free publicity.
Since Portman was already comfortable being topless among friends and acquaintances, it wasn't a big deal for her to strip down on the movie set, knowing that nothing would be released for public comsumption.
Mike Nichols and Closer win because they got most of the extra viewership that Portman's nudity would have attracted, plus all the people that only heard about the flick due to the news coverage of the "controversy". Portman wins because she can still expect extra money for her next FIRST NUDE SCENE. She'll still get this extra money even if they decide to release a later "Director's Cut" of Closer that includes some nudity, because most viewers aren't going to see this Closer nudity -- not theater viewers, not cable viewers, and not regular DVD viewers.
It's all a scam, guys.
--Curmudgeon