Bruce Wedlock replies: The obvious answer is to not let the glue/clamp/wood come in direct contact. The chemicals in the glue, the metal and the tannin in the wood produce the ugly black stain.
So eliminate the contact between clamp metal and wood. Put blue tape on the clamp where glue will squeeze out or lay some wax paper on the clamp surface. I don’t know about removing the stain other than scraping.