I always find clothed strippers in movies to be a stupid thing. If you don't wanna take it off don't play a friggin stripper.
First off, contrary to popular belief, strippers don't spend all their time at their job in the nude. Secondly, different states and cities have different rules about what an exotic dancer can and cannot show, whether it's keeping underwear on, having pasties to cover nipples, and yes, only stripping down to bra and panties. This also applies to the club owners - they control what strippers work, when they work, and what they do in order to reap the most profit (ie: you don't pay your best stripper to come in and show everything on a slow day). Third, strippers are people, too. And fictional strippers, like their real life counterparts, should be defined by their character and personality, not by how much skin they show. And finally, this is a MOVIE, and like all movies, liberties are made to suit the plot.
Source: I dated a stripper for several years during college and am still friends with many of her former coworkers.
I don't think it was appropriate to cast Alba if she was not prepared to go topless. The role called for that and there are many actresses who would have done the role.
The roll called for the character to work as a stripper, yes, but that does NOT mean the director and actress are bound to actually show her nude. Her being clothed did not negatively impact her character, nor the audience's understanding that she was a stripper. They made it quite clear without having to go the full monty.
To me, it seems like Alba was pulling a diva and made an excuse that her military dad won't approve of her so she couldn't do nude scenes, but in fact she probably felt like it was beneath her status to be naked on the screen. If she felt so strongly about it, why did she accept a stripper role in a R-rated movie based on a graphic novel where her character was nude in it?

You're assuming that the decision not to have Nancy nude was the result of Alba stomping her feet and making demands. Why must she automatically be labeled as a "diva" for choosing not to appear in the film nude? Never mind that nude scenes and sex scenes are a stressful thing - most actors will tell you that - but perhaps she has some modesty? She, just like every other person in the world, has the right to their body's privacy. Being an actor playing an exotic dancer does not change that.
If she felt so strongly about it, why did she accept a stripper role in a R-rated movie based on a graphic novel where her character was nude in it?
Ahem:
http://movies.about.com/od/sincity/a/sincityja032405.htm
Is it so crazy to think that she accepted the role because she liked the director, character and the script? You're also conveniently forgetting that the director CHOSE HER for the role, so it's clear he did not think that the nudity was vital. In fact here's his thoughts on it:
"'Like in the world of the comic, they just think that Nancy’s the sexiest person in the world and [addressing his comment to Alba] you did that. That’s all we needed. This works. It gets that across,' explained Rodriguez."
Obviously, neither the character, nor the success of the movie were dependent on seeing the character nude, so it really is a non-issue. They made it clear that she was sexy, and worked as a stripper. We don't NEED to see her take her clothes off to make that obvious, just like we don't NEED to see actual penetration to validate a film's sex scene.
I'm by no means a prude,nor do I throw up my hands in disgust when I watch films with nudity or sex. If that's what the director wants, and the actors are cool with it, more power to them. Personally, I think nudity for the sake of nudity is (usually) dumb and evidence of a poor writer and director, but if the plot needs it, it needs it. Conversely, if the plot/character does not NEED nudity, then there is no problem with the character keeping their clothes on.
It's rather sad seeing people here express their pubescent rage in not seeing Alba's breasts by trying to legitimize the complaint as if the character was totally dependent on Alba being nude, or that the lack was nudity is "unrealistic" and "unfaithful". The worst is saying that choosing not to appear nude makes an actress a selfish, whining prima donna. You're not fooling anyone and to be honest, these "legitimate reasons" are coming off a quite sexist. Seriously, if you want to see breasts that bad, go grab a National Geographic. I'd tell you to watch porn or get a girlfriend, but judging by these posts, I think some serious reconditioning is in order first.