When I skimmed through this thread I didn't see reference to any guidelines so I guess there aren't any.
I also think that animals (except service animals) should be in the hold. I don't have any negative experiences, but one of my brother in laws (GS) was transporting 'his' dachshund TCON J on a red eye - the dog 1/3 of the way apparently had serious diarrhea in it's soft carry bag/crate and he had to clean it out in the lav which apparently took forever and then when he sat back down the dog went again an hour later and he had to go through the same process (Flights have been diverted for this kind of thing). He doesn't even like dogs but he's the one who ends up looking after them.
The possibility for cross contamination is so high there is no way that humans and animals should share airline toilets so the only sensible policy is to put the animals in the hold.
Also I think airport comfort animals are a great idea for nervous flyers however IMO they have no business in the main cabin and the program as we all know is massively abused.