Mine weren't sticking out THAT far, but I just took them to the shop where they used the spinner and a bevel knife to trim/shave the pins back down, then cleaned up the surface of the ball.
I had a pin come completely out of a ball once. The shop just mixed up a bit of colored plug and poured it into the hole, just like plugging any other hole, and it worked out fine.
--------------------
"The difference between stupidity and genius is that genius has its limits."
Albert Einstein Good transactions list in my profile
My Bowl.com member page