We don't know that yet. But all signs point to yes. After all, we're seeing that:
The Governor is a depraved person and he has a serious sexual appetite. He first was shown in bed with the woman who was showing Andrea and Michonne around. Now he's in bed with Andrea. It sucks to think that he could make Maggie his next target.
It could happen. I didn't catch whether Michonne was with Rick and Daryl when they're presumably going to Woodbury to fetch Glenn, Maggie, and Andrea. If Michonne goes with them I think there's a huge possibility that they'll add in the rape scene.
With the world the way it is now I can't say I don't agree;
However the world HAS gone to hell.. so if he does rape her.. it wouldn't be too shocking..
Sad ? Most definitely.
Unpredictable of the ******** ? Nah .