First, let me start by saying that it sounds like your roommate is blowing things a bit out of proportion. That being said though, in all honesty, I don't think he should take the blame for the situation. From the way you described it, you were "assigned" to live with each other? This was not something either of you had control over?
I think that for the guy to even *try* to overlook Prada was more than should have ever been asked of him. Bottom line is, the complex doesn't allow dogs--you knew this in advance but chose to ignore their regulations. HE shouldn't be forced to have to live with your disregard too. It could be that he's concerned about being held accountable for any damages Prada causes....and if she's going potty in the house, it's highly likely that may end up being the case.
As others have mentioned, I would be concerned over her safety there with him. And if the letter really was from complex management, they will contact you again, but it would be wise to keep in mind it *could* be real and start exploring your options. YOU are in the wrong here and have a dog knowingly against their rules. They have the right to force you to leave or to get rid of her.