hmm, I am in a similar scenario. I went for my DODMERB Test to check my eyesight. I was told that I was color deficient. I thought about going to my own eye doctor because up until I took my eye exam for DODMERB I never had trouble distinguishing colors. Luckily I received a waiver last year, this year I will be going to a prep school before I go to the academy so my waiver is good for two years. Like your son I dont think I will be allowed to fly but I can vividly distinguish red and green, I thought about going to take the FALANT test which I believe is another test the ops use to test eye color, but I have since decided not to do so as I no longer wish to fly and due to the fact that I have a waiver and want to serve in the marine corps as an intel officer.
If you can, see what test your son took and then check to see if there is an alternate test that judges the same ability as the one he took with the DODMERB op, or check to see if his condition is correctable (surgery). You can also wait and maybe he will be lucky enough to get a waiver.
I hope everything goes well.
