C.B.
My girls hated baths from day one and only liked them a bit better when they sat between my legs in the tub. So initially (after really young infancy baths) bath time was with mom. Eventually they got more comfortable and were able to be in the tub without me in it, and later both girls together.
How about filling only a very small layer of water and letting him stand in it while you quickly sponge him off? Or if you have a hand-shower (or you can attach one of those to the spout or get a shower head that has the hose with the handheld shower) then you can spray him down without getting any water where he does not want it, maybe starting just with "tickling" his toes. Or he can direct the water where he wants, even if it is against the wall for starters.
There is also no problem with simply wiping his privates and hands and feet with baby wipes and a wash cloth for his face for a few days or weeks. I would change pediatricians if that is his advice. Why traumatize a kid over something that is not essential (since there are other ways to keep clean)?