Looks like you've gotten tons of replies, I haven't read these.
There's good herpes info available through the University of Washington Virology Research Center.
Herpes can be active and contagious with no sores present, and a person can have the virus and be contagious forever without ever having visible sores. It also pops up awhile after exposure. So it wasn't necessarily his Dad, and you won't ever know for sure who it came from.
Given that the virus goes dormant in the nerves, then becomes active and trots back out on the nerves to the skin, where it kills skin cells, the diaper environment probably has nothing to do with the activity of the virus. Stress is a more likely culprit.
Monolaurin and the amino acid lysine are helpful, and the amino acid arginine can trigger outbreaks. I've seen the brand Lauricidin help with cold sores a lot. You might have to check with a naturopath for help with dosing a little one though.
I understand it should get better with time, as his body builds immunity.
As for the skin, Herb Pharm Trauma Oil might help. It has calendula for healing and hypericum for pain. I used it on my son as a newborn with my midwife ok but use common sense caution on deciding if it's right for you.
Also, Hylands Teething Tablets or Calms Forte might help. They have pain relieving ingredients and help a baby be less angry about not feeling well.
For the diapers, good wound care is important. Consider that urine is sterile and helps wounds heal, and air is good. Sposies don't help with that! Cotton, plus wool or fleece may be your best friends. I wouldn't put anything fragranced on him, and zinc won't help wounds heal. Treat it more like a cut, IMO.
I wonder about sitting in water with sea salt and baking soda, like the neti pot mixes... Baking soda cuts the sting.
And rubbing him with olive oil at each change may help make it easier to clean poop off when the time comes.
So sorry you're having to deal with this, and the unnecessary stigma and criticism.