It kind of depends on the rest of your bedding. Is it full contact with pillars, or floating on pillars? It may set up some weird stresses in the receiver if the screws are pulling in slightly different directions. (One pillar straighter than the other or something like that.)
Personally I think i would drill them out, scrape the bedded area and take another shot at it. If you're worried that you don't have any reference points left to square up to- use layers of tape around your barrel to match the contour of the barrel channel. Get the stock set up in a padded vise, use the barrel channel to get the action square front to back, and up and down. A level across your scope rail or other reference point, and your bottom metal to get the vertical back to square.
Build dams with modeling clay to prevent run out of the bedding compound and then redo either your pillars alone to get a reference point to work from. Or do the whole thing over if you feel confident that you can get the action realigned within your compounds working time. You can also tape the screws off like the barrel to make them fit your pillars tighter if you need something to keep them aligned.