A 500 can run quite well with lots of pistion issues. Two years ago, my oldest seized a piston in a brand spankin new KX500 on practice day at a National in California. Upon checking, it had a score all the way up one side about 1/16 deep and 1/8 wide. John had an extra cylinder in the Kawasaki semi, so we swapped off to a new cylinder. I later used the old cyliner with the score, and was shocked to find that there was almost no noticable power loss. For the average rider, they would never notice anything. In fact, the bike is still running the same "damaged" cylinder two years later. I also ran my 1999 KX500 cylinder too long, and found the plating on the exhaust side worn badly. Here again, little noticable power loss.
With all that said, as long as the slight damage on the piston does not effect the ring's ability to compress smoothly, I would use the new piston. If we were talking about a KX125, I would have a completely different oppinion.
Good luck
Rick