With surgery there is a risk of damage to the rectal wall. This is usually repaired and is not a major problem. Chrones disease does raise the potential for an increased risk, which makes it more important to consult a top surgeon. Choice of surgeon is always a more important consideration than the method of surgery used.
Personally I'd be circumspect about seeds in the circumstances, but again you could get more details from a top specialist.
Proton is well targeted, but it might not completely eliminate potential for rectal damage. It could be worthwhile consulting Loma Linda for their view on your case, or asking Bob at the protonbob website.
Depending on your full diagnosis, there's a lot of information available on watchful waiting criteria in the meantime.