I'm not sure about the gripe against newspaper. Sorry you are going through a tough time with snake illness. One of my new acquisitions came to me with an RI that I'm now battling (going into the vet tomorrow for a possible second round of antibiotics) and it's never fun. I agree that using a sterile substrate is best, but only within reason. I also don't think I'd use printed or old newspaper as a substrate, just because newspaper gets damp easily and can be a source of mold. I like the rolls of indented kraft paper for my substrate. They are a little thicker and absorbent.
As for keeping snakes healthy, I think the most important things are keeping them quarantined when new and keeping their husbandry correct.