It ended today. I think PZ Myers did a good job ending the whole saga. It's pretty eloquent, I'd say.
While I have no interest in helping Catholics further rationalize their delusional beliefs, I want to explore a line of argument open to them (disclaimer: I was forced to attend Mass until the age of 15-16 and refused to go through Confirmation). I think there's a way that a Catholic could come away from the cracker dustup not only being but also looking like the better man.
First, the Catholic must recall that most of the world is not Catholic. The rest of the world, theist and atheist alike, care nothing for Catholic dogmas and sacraments. Try explaining the details of Transubstantiation and Communion to anyone who isn't Catholic (or Lutheran or Episcopalian maybe) and they will find it all ridiculous and/or gross. This is just a cross you'll have to bear. You can try to bear it in some kind of Christlike manner (I'm not making any recommendations here!) or you can react like Bill Donahue.
It's important to remember how this whole thing started. There was no theft or even malice on the part of the student who took the communion wafer. It is Catholics who reacted monstrously.
The proper response (in my advice to Catholics) would have been not to respond monstrously to the initial incident. Whether out of ignorance or malice, people are going to insult your beliefs--live with it. And think how many actual communion wafer desecrations the Bill Donahues caused by their intemperate reaction to the guy who tried to walk off with his communion wafer to show a friend who was curious about Catholicism.