Great minds think alike Nate - I was thinking about this overnight and had the same reservations - And came to exactly the same conclusion/idea
Assuming the holes are still narrow enough to hold the pins in place (it seems to be the case for at least three, I'm not sure for the top right one), I wouldn't bother with filling them prior to peening. Once peened, you can fill the remaining gaps (if there are any) with nail polish of matching color. It holds quite well and can easily be replaced when it falls apart.