Here's a thread talking about a Cummins 4bt in an MJ (sounds like a lot of expense/trouble, but it can be done):
Link
From what I've read, Cummins 4bts and 3.3 were used in a lot of delivery trucks & bread wagons, and some shuttle buses. So while it'd require a lot of hunting, you can find 'em in junkyards.
And here's a forum that has tons of info on Diesel swaps in general:
Diesel Page Forums
I have a full-size J20 with a very tired 401 in it. I'm currently gathering parts and searching for a suitable donor so I can go with the GM 6.2/6.5 diesel swap and turn it into a fry-burner. For the big truck, it makes tons of sense - the 6.2 and parts are readily available, everything is pretty much bolt-in, and people who have done the swap are reporting average mpg's in the mid-20's while still being able to work it like a full-sized truck should be.
From what I've checked out, the 6.2/6.5 shares all the same mounts/dimensions, bellhousing with a SBC, and is about 200lbs heavier. I've seen people dropping SBC's into MJ's and XJ's - so I'd think 6.2 into a MJ would be possible as well - but IMO that's a lot of work/expense and extra weight in the front to deal with. So unless you're just truly a diesel fan, I don't think it'd be worth it.
Depends on if you're looking purely for mpg or the ability to home-brew your own fuel.
I have a 2.5L 4sp MJ that I use as my DD. I've found that as long as I keep the engine well-maintained and drive with a light foot, I'm already at 30mpg in mixed driving. At one point I considered a diesel swap for the MJ, but decided that after the expense of finding a suitable donor and the conversion work, any savings from increased mpg and the cost difference in diesel would be years down the road.