I rather like the idea of this setting, but I'd prefer to implement it in such a way where the humans are still around, just in absolutely puny numbers. In my mind, isolated groups of humans might have survived the end-times, being so utterly out-of-the way that the disease, which mainly was aimed at the great kingdoms of humanity, largely passed them by. Most of the villages would still be wiped out, but mainly because of refugees that passed through, bringing the plague with them. therefore, a few smaller towns might have made it, and have kept themselves secure by either getting paranoid (shooting everything that moves) or hiding (going underground, to where other survivors won't try to look for them, and only occasionally hitting up the surface world for the important stuff, like medicine or weapons or arcane scrolls).
The problem starts when these surviving humans take a look at what's become of the surface world that they abandoned. To their dismay, the humans find their towns taken over by the 'Forces of Evil,' with Orc tribes running rampant through the empty countryside and kobolds and gnolls and whatnot taking over whatever they feel like taking over. Essentially, these humans survive, but only so that they can see the destruction of all the things that their species created and made great.
I think that playing a human explorer (essentially an arcane S.T.A.L.K.E.R., who was fortunate enough to be in the negligibly small group of people who are totally immune to the plague) who as to band up with a team of 'lesser races' would serve as a pretty nice setup for the campaign- maybe he's contracting out these Orcs and others so they can help him go to his family's old home and gather some of their heirlooms, that his parents had left behind when they fled their homeland.