I admit I don't know the first thing about snakes - when you talk about hybridizing you are talking about breeding two different species?? If you are - then you can't use the cat and/or dog argument. Crossbreeding cats/dogs can be liken to breeding different colour morphs - not breeding two different species. You aren't creating a new species when you breed a poodle and a boxer - just a morph, but still a dog.
I agree with Lindsay - creating hybrids (which is a rarity in the wild) puts a species at risk. If wild populations are decimated and captive ones are hybridized - that species is gone.
Breeding for albinoism/colour may certainly weaken the gene pool - but we also breed for non-agressive behavior and lack of fear. The colours and temperments we are culturing are not for the benefit of the wild animal. Bright red bearded dragons and chameleons that are docile would not survive in the wild. I'm getting a little off topic - but the average keeper cannot expect to produce animals for captive realease. Captive release programs must be closely monitored to produce animals that will thrive in the wild and not put indeginous animals at risk (either through disease and/or behavior). That being said, captive propagation does lessen the strain on wild-caught populations (obviously!).
So, by breeding for colour and temperment we can increase the "attractiveness" of CB over WC. Breeding for a new species is not necessay - that kind of activity is up on top of my "scary" list along with cloning. We have no business playing there - it crosses over the line.
If I'm correct in assuming you're talking about breeding two different species - are the offspring fertile? Or is it like breeding donkeys and horses?