Granted, I don't think the issue of Affirmative Action is quite as simple as this, but I think that the College Republicans' bake sale served as a fairly reasonable example and a clever way to make their statement.
I find it sad that the people who disagreed with them had to resort to near violence. The only thing I could find that they did wrong was that they were deceptive in their application for event space at the college.
As far as that goes, I think the university has as much right to require protests/protestors to be in designated areas as the president has to restrict them to "free speech zones."
But again, as far as the students go, I think they made a clever statement, and they weren't hurting anyone with their bake sale.