Is this input shaft pitted inside or outside of the trans case?
If its outside the case, on the splines, as long as the clutch disc can slide on and off the shaft without hanging up, it will be OK. Inside the bearing retainer, the shaft only has to clear the bearing retainer. If your referring to the bearing retainer, the throw out bearing needs to slide smoothly across it and it will be OK.
If the pitting is inside the case, as long as it doesn't interfere with the gear operation it will be OK.
It would have to be pretty serious pits before I was concerned.

Bushings are a little more forgiving if everything istn't lined up exactly, but I've used both bearings and bushings. Gene