Humans find it hard to think on Evolutionary terms though, it's not very comforting for someone to know that, although they are dying from MS, that in a few million years time, we will probably be immune to it. I suppose there are arguments for and against the use of medication, from a purely personal level, it can save your life, from a longer-term, wider field point of view, it might be a fuse that we've lit, and we aren't even sure what the barrel contains. Bacteria, at least those that are frequently in contact with humans are no longer entirely at the whims of natural selection, as we come up with more and more powerful treatments, so the survival conditions get harsher, which produces more and more hardy strains of bacteria.
It's sort of like an Arms Race, it's been theorized that it would be impossible for a disease to wipe out any species entirely, because immune systems were evolving as quickly as the diseases, personally, I think that's where the future of medicine lay, not in supplying the body with a pill that kills the disease, but more on innoculation and resistance to the disease in the first place. I think if we become too reliant on 'pills', we are leaving the immune system too vulnerable to the more hardy strains of disease.