Just to add that unlike what would seem expected behaviour, 'SetEnv SAVE NoTrance 0' (and reboot) won't turn Trance on again because to decide whether or not to start Trance, startup-sequence only checks for the existence of the NOTRANCE env variable, not for its content. So deleting ENVARC:NOTRANCE is required to permanently turn Trance on again.
It would be interesting to know why you want to turn it off. I've found the JIT pretty much problem-free since MorphOS 1.4. Are you debugging something low level or running benchmarks?