Crypto is an intestinal parasite that follows the fecal/oral route of exposure. The animals must actually ingest a small amount of infected fecal matter or oocysts that came from feces transferred to another surface.
This can be as easy as handling an animal, scratching an itchy nose, and then scratching that same itch later on before handling another animal, though that's a pretty extreme example. Even with careful handwashing it is possible to infect something in your home and then reinfect your hands at a later date. You have to be hyperaware of your behavior. Working in operating rooms for 17 years gave me some experience with this, but it can be tough. Never touch any surface that is not the animal, its furniture, dishes, supplies, etc. once you are gloved. Not even the cage door! If you do, immediately toss gloves, rescrub, glove again, and disinfect what you just touched. Then deglove, rescrub, and reglove. That is true sterile technique.
Definitely a separate room, separate dishes, utensils, furniture, etc. Disposable non-latex gloves worn during all feeding, handling, cleaning, etc. and immediately discarded. Latex allergy is what caused me to become disabled and herps can develop the allergy as well as humans so consider never using latex and avoiding that whole mess.
I don't personally take in known infectious animals and test for almost everything when I bring in rehabs. Almost all of mine are recent post-ops so it's critical they not be exposed to anything, not even common bacteria like staph and strep. But I would still not destroy an animal unless it's in distress. I'd just empty another closet, buy a new HEPA filter to avoid airborne contaminants (not that crypto is airborne but they often get secondary infections) or find somebody I trust to do the same.
The Zombie Mama is here!