So if carrying a pet within the aircraft cabin raises an in-flight allegy problem, which are they going to send outside to sit on the wing?
The pet or the allergy sufferer?

I think it's great small pets are allowed in-cabin on flights. You can never be guaranteed the conditions in the hold. As for pets disturbing the flight, I don't think it's an issue. I have been on multiple flights (transcontinental and transatlantic) in which cats and dogs have been in the cabin. They didn't make any noise that I could here. The one question I have was how they deal with the need to go to the bathroom, but I assume that the animals are not fed much before the flight.