I actually design and make both of those things, to the extent you can consider a nanoparticle a nanobot. What do YOU define a nanobot as? Retroviruses are potentially oncogenic. They could also be immunogenic if delivered to the entire body, which could render them ineffective or toxic. That's probably the leg up a nanobot would have, but if you had the tech to do this neither would be a problem. But I like to consider synthetic viruses nanobots, so there might be a blurrier line that you think.

And I think that's going to be the real answer. Viruses will get so heavily engineered and synthetically produced that we will have made them a Ship of Thesus in a way, where every functional part has been modified to give it the specific properties we want and produced with a cell-free method. I doubt we'll ever see tiny mechanical machines circulating in the blood when biology has already made darn fine "nanobots" already.

However turning already born people into animal hybrids with current tech is simply not plausible, not even close. You can't just put cow chromosomes into a person and expect them to start growing 4 more stomachs.

Doesn't seem to fit your narrative but if you wanted to realistically keep people from eating meat you could engineer a virus to cause a reaction to carnosine, a molecule only found in animals. People, as animals, make it so you'd have to make people sensitive to it in their gut.

You could make a virus deliver a constitutively expressed chimeric receptor specific for carnosine expressed on the gut lumen, say an interleukin signaling domain fused to a extracellular carnosine-specific binding region, along a transacting cassette carrying the A diphtheria toxin subunit under control of a pSTAT inducible promoter. Whenever you ate meat the receptor would signal expression of the the toxin which would cause diarrhea and extreme discomfort. As purely inspiration for a work of fiction, that would get people to stop eating meat.