Really the only answer to this question is "Eventually." End War is certainly a step in the right direction, what with the voice command and all that. Until we get really, really perfect voice technology (does that exist yet?) then the RTS will remain on your PC.
I just can't see how you could easily select units with a console controller, or move your cursor fast enough, other than a totally new controller or through voice. Still, screaming orders into the mike might be kind of fun. Unless the voice command interperets it wrong.
You might be able to do a good RTS with the Wii controller, now that I think about it. The thing acts like a mouse sometimes anyway, it's not much of a strech to make a good RTS with it...
Damn, now I want to change my vote from Eventually to Yes. I need to stop overthinking these things.