Not all allergies are like that. I would wager the vast majority are pretty mild symptoms easily treatable with anti-histamines. I myself have allergies, but I never even notice because the air at work is filtered and I'm not outside long enough for symptoms to manifest as I travel to and from my car.

Maybe the case could be made for fighter pilots (though I still think it's a non-issue for 99% of people with seasonal allergies), but what's the excuse for disqualifying for all aircraft? Airline pilots can have allergies and fly. How is that much different from a heavy cargo plane?