Since OS4.x already has a JIT, is there any way in which Petunia could be employed for the purpose of emulating the 68K?
In practice no. Petunia (and Trance) try to be as fast as possible. Adding some address translation and trapping of specific addresses (custom, cia etc) to all memory accesses would generate ton of extra code. In any case it would require a lot of work on the actual JIT engine itself. This is unlikely to happen.
For any OS component to be usable for GPL application it first needs to be released as part of the OS. Also, releasing such update just to circumvent the GPL license would not be seen as very sportsmanlike I'd think.