I have those pedals, and I understand the problem that you are describing - I noticed it the very first time I rode with them. After about 1.5 years, I have concluded that it is not actually a problem.
My slightly older XT pedals do not have these seals -- I know this conclusively, because I have dismantled two pair of them for cleaning and regreasing a couple times. The spindle just fits inside the pedal body, with no rubber seal. So, on the newer XTR pedals, the seal is an additional item. Yes, it should stay where it belong, but it doesn't -- and that doesn't seem to harm anything. My XTR pedals, even with the seals working their way out periodically, are holding up better than the XT pedals without the seals. (And by the way: if you are worried about dirt and water in the bearings, it is pretty easy to overhaul those pedals. Look for the Park Tools video online.)
My only concern about your solution is that the pedal body needs to rotate on the pedal spindle, but the JB Weld could bond them together...Unless I am not understanding precisely what you have done?