I would think you can change the barrel to whatever you want, unless Ruger uses their own proprietary parts...which really wouldn't surprise me. .300 whisper would be just a barrel change, but you'd have to change the bolt and barrel to do 6.8.
On the other hand, Ruger isn't the only name in AR's. You could probably pick up a DPMS or Rock River built the way you like it. I know both make hunting models in 6.8. .300 Whisper might be hard to find in a hunting model just yet, since its supposed to be a "tactical" round, or whatever they call it. Anyway, I guess I'm saying you could get a complete rifle just the way you want it, without the trouble of changing the barrel out.