IF I make the mclr pin an input will the pic still program ok If i just oplug it into a programmer? I wont disable it's ability to be programmed if all pins are designated inputs or outputs?
The only thing to watch out for is the high voltage (13 v or so) on MCLR during programing. Some sort of isolation is all that is needed . Anything from a diode to a switch. Remember, MCLR pin can only be an INPUT.

You have the PICKIT2 docs? There are isolation drawings there and I think on the PBP web site.