Sure it's POSSIBLE... the question is, how much work and/or money do you want to dedicate to it?
I looked at doing an auto-to-manual swap on an '87 Accord a few years ago (wanted the car, didn't want the auto)... it's not quite as simple as just unbolting one tranny and bolting in the other. In that case at least, I would have needed to swap the computer as well, and possibly change a couple of connectors on the wiring harness (like the one for the alternator). As I recall, I would have needed to replace one of the CV shafts as well (one side was the same, other side was shorter with the 5-speed). And there's always a bunch of little things, like the console section where the shifter lives... etc. etc. etc.
Not saying that the same job would be as complex with the Jeeps, but there's always more to it than just removing one and dropping in the other.