We no longer need advice, and he'd rather not have info about his personal areas out on the web.
Sorry, I can't tell you if this is serious or not. What is your son's pain threshold? Is he running a fever? Green pus usually means infection to me and I would treat my child the same as I would for any other infected skin condition. . . with a careful eye on making sure there is complete healing.
My boy is only 6 months old and I have not had experience with what you are describing, but I know what I used when my girls had yoni irritation/infection/rashes and how I would adapt that to my boy if it did come up. I would make a tea of white oak bark and echinacea (equal parts). 1 teaspoon dried cut and sifted herb for each 8 oz water. Simmer 15 minutes. Strain and keep in fridge up to 3 days. Warm it to just warmer than body temp and then put it in a baby food jar or shot glass and then use a larger narrow jar or glass that would work for Dad. Then put on an audio book or movie and have Dad and son sit for 10 minutes doing a penis soak in the warm tea. Repeat at least once daily and continue until 2 days after the pain/irritation/pus disappears.
If Dad and son are not up for doing the penis soak, I would keep a bottle of the tea in the bathroom and have him apply some of the liquid with a clean cotton ball every time he pees.
White Oak bark is an astringent. Other herbs could be used if you can't access it: Red Raspberry leaf, plantain leaf (not the banana plantain), yarrow leaf, manzanita leaf, or even black tea.
Some use diluted apple cider vinegar in the same way. 1/2 teaspoon in 1/2 cup water