The protocol used by my surgeon included a MRSA swab as part of the pre-op exam and all patients are required to use Mupirocin twice a day for 3 days prior to surgery. I suppose the idea is to minimize any possibility of picking up an infection in those last days before surgery. But I guess Mupirocin can have side effects so unless there's clear proof that patients who use it do better, I can understand a doctor choosing not to prescribe it.
This is just my personal opinion but I think you have to remember that "old and run down" doesn't necessarily mean "unsterile" or not as good. The hospital system that my surgeon is part of has a brand new, state of the art facility - it's only 5-6 years old and at least one other surgeon in the orthopedic group does his joint replacements there. But my surgeon, who is the Chair of the joint replacement program, will only do replacements at the old, main hospital in the surgical suite that he designed. I want my doctor to work where he's the most comfortable and successful because in the long run, I think that translates to the best outcome for me.