I picked up a used set of LS1 heads to modify. I am wondering if using a bead blaster to clean up the gasket surfaces and combustion chambers is a good or bad idea? Thanks

Bad idea. Clean them with lacquer thinner. If the surfaces have been badly mared you should get them resurfaced.

Bead blasting is done all the time to aluminum heads. Just don't hit any machined surfaces that aren't going to get re-machined. In other words, guides, valve seats, deck surface, etc. If your getting the heads resurfaced and the seats recut, then it doesn't matter. And be carefull to completely clean the heads afterwards.