Well I remember back when they first announced XNA, which is their big developer kit/package/program, that the goal was to have games playable with PC's as well as with devices like PDA's.
I remember one example they used would be a person playing a Real Time Strategy game on the PC, where he is in fact issuing the commands to people playing in the first person on 360.
I think that if such things like that are part of their ambitions, then certainly we can expect some straight up PC and Xbox online play together as well.
It would still be over Live though, and you would have to subscribe to Live for PC, when/if it ever becomes available.