My strong suspicion is that this is a political prosecution, orchestrated by the school's administration in order to placate a bunch of conservative rabble-rousers. There's also the fact that the Catholic Church has a lot of influence in Pittsburgh; some of this influence comes from their ownership of a lot of land in CMU's neighborhood, which gives them influence over local zoning ordinances and would allow them to refuse to sell said land that CMU might want for future expansion.
There are two lines of evidence for my suspicion that this is not simple law-enforcement. First, it seemed to take a long time for the police to charge this woman. I'm sure that cops were present during this parade, and they could have issued her a warning or citation on-the-spot. The fact that they did not immediately issue a warning suggests that nudity is tolerated under these circumstances.
My second line of evidence that this is a political prosecution comes from various reports that nudity has traditionally been tolerated (if not encouraged) at these parades. I read this claim in the comments section of an article posted at the website of the CMU student newspaper, the Tartan when this all started. I followed up by looking at the official promotional material for this parade. Notably, the pictures from the 2013 parade have been removed from Flickr. However, the 2012 parade pics are still available. They make it clear that the parade is typically pretty raunchy (facebook shows a subset of the more tame photos). There are even a couple of pictures showing exposed buttocks (and ass crack), which falls foul of most indecency ordinances that I've looked at. For the sake of documentation, I'm going to repost the picture here, though I must warn you that it isn't pretty (original):