While I don't think it's a bad idea to microchip animals with a specific ID and genetic information...I personally don't believe it would help with the arguments against hybrids.
It all boils down to accurate record keeping. The responsible keepers will do that. But once they sell their offspring, they have no control over who eventually ends up breeding them. If the irresponsible breeder isn't going to bother keeping written records, then they're sure not going to bother with the fuss and expense of microchipping.
I don't find anything morally or ethically wrong with the practice of breeding hybrids. And I don't think a few difficult-to-breed unique hybrid combinations are going to ruin or "taint" our lines of ball pythons or blood pythons. But there ARE some hybrid combinations that I can see this being a genuine concern for the purists among us. And for them, I would also suggest microchips and accurate written birthing records. Not much else you can do, that I can see.