I've spoken with several ex-military folks and most of them agree that this will not cause any catastrophic problems in the military. There will be issues to deal with, and some additional costs involved. I think it will also increase the amount of harassment to gay people now that some of them will "come out". But the vast majority of military personnel will follow orders and do their duty as before.
My big issue is with congress sticking their noses in an area where they didn't need to. This was purely a politically motivated decision, they were pandering to a certain voter base. Whether this is the right or wrong thing to do, it should have been left to the military commanders to make.