What about using a cream-bleach cleaner like Soft Scrub with bleach? It's thick so it would adhere longer to the surface. And if you scrubbed with a strong brush immediately after applying it, you could really work it into the "stain."
I realize that it's not ideal to add "cleaners" and their various chemical to your pool, but if you used just a little and wiped up the excess, I'd think the rest would be so diluted that it couldn't hurt.
Of course, I'm no expert so I would wait to see what everyone else thinks about this idea!