I use a friends 14' aluminum river "sled" boat once in a while,, and mount my electric troller on the port side for the reasons you mentioned. It steers differently than with the outboard mounted on the transom, but it's not too bad. This is a river boat, with no keel, and steerage is a little tricky with no current to work with anyway. I would expect a jon to operate better, even with the motor on the side, as all the jons I've seen had a pretty good keel, or even several ribs running the length of the boat. this should give the boat good "direction" and what you plan to do should work O.K.
Try it, nothin' bad's gonna happen.................................ModocDan