Can I disinfect my Apple Watch with Isopropyl Alcohol wipes?
Yes, you can, but doing so is obviously not in accordance with Apple's instructions. All that means is that no one can provide guidance regarding its tolerance to long term use.
My Watches have come into contact with a wide variety of solvents including alcohol, gasoline, motor oil and other contaminants with no adverse effect, so I can say that inadvertent contact certainly won't harm them. Long term or routine use of isopropyl alcohol specifically for cleaning and disinfecting them might cause cosmetic or other damage that Apple simply hasn't tested.
When cleaning them I just run them under lukewarm water and dry them with a soft cloth. I would tend to avoid using alcohol on the fluoroelastomer band because it's been my experience that alcohol tends to cause rubber to become hard and brittle. Fluoroelastomer isn't rubber though, so perhaps it will bear up better.
How do you disinfect other wristwatches that you have worn in a hospital environment? If you have been using alcohol with them without any adverse effect, I doubt the Watch will be any different.