No STD is likely to have been transmitted by genital apposition without penetration and a doctor confirmed you didn't acquire an STD.
Women get burning and itching of the vagina all the time. Most cases are not due to STD and yeast is the most common cause, which was confirmed in your wife. Yeast can cause red bumps of the penis. Those bumps can clear up in 2-3 days, but herpes lesions cannot; it always takes at least 7-10 days for herpes lesions to heal.
The problem obviously is yeast, not herpes. Your wife should follow her provider's advice and use the treatment that was prescribed. Once she does that, your symptoms will stop returning. You probably do not need treatment yourself.
Good luck-- HHH, MD