I re-read your OP and have to say I think I agree with your allergist about the sinus surgery. I definitely sympathize with your son, but I don't feel his symptoms, as you've described, warrant the risks of surgery, and yes, there are always risks with surgery. Sinuses are near the brain and facial nerves, spinal fluid, etc. You make the sinus surgery sound like it's no big deal, and perhaps you were given that impression. But I think you'd be wise to listen to what your allergist is telling you "between the lines". He didn't just drop off the turnip truck

and I guarantee he has seen things he is not telling you specifically about; instead he's summing up his experiences by saying he doesn't recommend it. Listen to him! (IMO)
I remember when my DH was in surgery (at Mass and Eye and Ear in Boston) and the surgeon came to the waiting room to update me to say she elected to not touch one area of his sinuses "because it was too close to his brain" and she "didn't want to risk it".

I mean, we know these things going into it, but it drives home how serious it it when you hear something like that, or God forbid, if something untoward happens. Hindsight is 20-20. If I did elect surgery, I would make sure I knew every detail about the risks going into it, that the benefit far outweighs the risks, and I'd make sure it was being done by the best person at the best facility, etc.
I know this isn't the exact surgery your son is having, but it is the the typical type of sinus surgery and shares some similarities to the one your son will be having. I was searching for info for you about the risks of sinus surgery, and came across this "brochure" that I thought might be informative to you and help you formulate questions about your son's procedure.
http://childrenshospital.org/clinicalservices/Site2149/Documents/SinusSurgery_121608.pdf Also know the ENT may very well recommend some of the meds for him post operatively that you've already had him stop taking, so I'd ask about that, for sure. (And if you don't take them, you become "non-compliant", so follow up may be tricky if he continues to have problems, which many sinus patients do.
http://www.kids-ent.com/website/pediatric_ent/sinus_children/index.html )
My gut sense after reading this thread, and because I know you want to get some relief for your son, would be to go back to "Phase 0" with him, as if you're starting all over again. Wipe the slate clean. Find one physican to work with on it, have a heart to heart ahead of time, and start again, knowing what you know now. That is, I would try a PPI, flonase and a decongestant daily, along with other methods to prevent allergens from negatively affecting him, and this will be multi-factorial. I would give it a good month or two or three before deciding it isn't working - maybe longer.
My DS, who is 16 soon, has a good treatment plan that works for him when he follows it. As a typical teen, he doesn't always take his meds until he's in distress. Not a great way to manage things, and as he matures, he sees it. (Not saying this is the case for your son.) I do try to keep his meds on hand and I've put them all in an accessible place for him so there's no excuse for him not to use them. When he has flares and we wind up at the doctor's, we're honest with them about his not taking his meds regularly. He's learning. At any rate, sinus surgery is not even on my radar for him at this point. Again, I know this seems to be different for your son, but just throwing it in there to say, I can relate. I know it's a strong opinion (about the surgery) but I'm assuming you're looking for opinions. Good luck with whatever you decide. It's tough to see our kids not feeling well, even when they get older.