Anoxia through O2 starvation is demonstrably painless. Many research pilots go through it, to the point of unconsciousness, and the general comment on recovery is "Did something happen?"
CO2 overdose triggers the breath reflex, which O2 starvation does not, at least in humans.
I did a fair bit of searching, but all I could find was protocols describing various euthanasia methods. I couldn't find anything that motivated them. Sure, I found some discussion of why toe clipping is discouraged, but that's because toe clipping isn't The Method for identifying mice (anymore). CO2 gassing appears to be one of The Methods, if not The Method, for euthanizing a bunch of mice -- hence, not much debate or discussion.
I don't know how many readers I've got, but I'm throwing the question open: who decides what the `official' animal protocols are? (Does it differ if you're a university vs. a company?) How do new methods get invented, approved, and adopted? What happens when an alternative method gets officially discouraged/banned? Where can one go to find out all this information about a specific protocol? And if it's the case that O2 starvation by N2 surfeit is painless, why isn't it The Method?