I ran a turboed '94 6.5/4L80e in my S10 for years. It was quicker accelerating with the 6.5 than with the tbi 350 it replaced even though it gained 1500lbs with the upgrade to 1 tons with the diesel swap. I've since pulled the 6.5 for a D-max, but for drivability and fun factor I would much rather have stayed with the 6.5 over the small block.
There are some things that concern me about your ideas though. The main one being the unibody vehicle. I also agree that you will be playing with fire with your current axles. One other thing that you may want to consider is the shear size of the 6.2/6.5 and the Duramax, they are HUGE compared to a sbc, I have comparison pics if you'd like to see them. It will also be difficult to get a large enough radiator in the Jeep, much less an intercooler. Something to consider any time you are going from a gasser to a large diesel is that nearly eveything in the entire vehicle has to be modified to accomidate the extra weight, torque and cooling needs, ask me how I know, lol.
Good luck with which ever route you decide to go with and be sure to keep us posted.