I don't mean to be a scaremonger, either. I say you know your son's abilities better than anyone here, and as such you can make that judgment. As a junior that means he's 16, right? I'd have no issue letting my own child take such a journey when she reaches that age, but you just need to make sure with the airline that they're not going to throw up any flags. If he's older than 15 he's not able to travel as an official airline-escorted UM, so that would lead me to believe that they don't have an issue with a 16 year old traveling alone.
Edited to add: your logic is sound but I hate that schools try to take over what should be a parent's decision anyway, in terms of attendance.