I understand his resistance to taking medication. I don't like medication myself. However, the antivirals have a history of being safe to take, and will most likely help him tremendously. There is no need for him to suffer.
Headaches are not a common symptom, but I do know some H+ people who get them. However, his headaches may be caused by stress from the diagnosis. Stress is a common trigger for outbreaks. I highly recommend he find ways to manage his stress.
There really have not been any reliable studies on "natural" remedies that have proven a definite impact on the virus. Lysine has been shown to have antiviral properties, but there have been no clinical trials on delivery methods that show any kind of reduction in recurrences. Lysine did not work for me, nor for many HSV+ people that I have met. I strongly urge him to get a prescription for the antivirals.
Yes, this is genital herpes.
You're saying he has oral herpes or genital herpes?
The headaches if they are related to the herpes may be due to the virus roaming the body during early phases of infection and/or the building immunity.
The antivirals are super effective at addressing the headaches if they are caused by the virus. Once his immune system has reached optimal levels, its unlikely he will have these issues.