**"Including non-HSV babies."
Odds are you both have the virus. The question remains, which type? Have you ever had a cold sore before? Many people have HSV1, which typically is contracted at childhood.
If you have oral sex, odds are she has HSV1 which is on the rise for genital infections. The goal here is to have the bumps swabbed and have a blood test to see who is positive for what and what types. From there you can game plan.
If you both have the virus, protection is useless as it would be insignificant because you both have antibodies for the virus. If she has HSV1 genitally and you orally, it would be extremely unlikely you contract the virus in a second location (ie. genitals). This is due to the body already having antibodies. This includes when she is having a breakout. It's that difficult to transmit when the host already has the infection in another location.
Please get blood tested via IGG and go from there. This doesn't have to be a relationship breaker, many people have HSV and live perfectly fine lives with healthy sex lives...including having healthy non-HSV lives
Wow that's terrible diagnosing by the doctor, most incomplete! Did he not even take a swab??
The place seems wrong and you can't just visually diagnose with huge confidence. It could be shingles (and the doctor probably implicitly included this possibility in his herpes diagnosis), fungus or bacterial infection.
If it is herpes, then an example of how it happens is that you have an oral HSV1 infection and passed this to your wife's genitals through oral sex. This is very common.
If this is important to track down, then you should both seek IgG antibody testing type specific for HSV1 and HSV2.
Regardless of what you decide to do, both if you reach the place that you are dealing with one of the world's most common and in most cases insignificant viruses that pales against a loving relationship.