yeah that was some SWAG on my part...
my guessing was posing as logic and telling me that the 2 gaping holes in the 3 door would be better than the 4 gaping holes and overall greater open area on the side of the 5 door. the argument posed by iBran about the b-pillar being centered in 5door/sedan configurations does make sense though. i haven't found anything specifically about the cherokee but here are some numbers for another car:
sedan 18,000 N-m per degree of torsion (100%)
sport wagon w/ fold downs 14,000 N-m (77.8%)
sedan w/ fold downs 13,000 N-m (72.2%)
coupe w/ fold downs 12,500 N-m (69.4%)
convertible 10,500 N-m (58.3%)
there is no direct comparison here because there would need to be a 3 door wagon to compare to the sport wagon. notice though that the coupe, sedan (with fold downs) and wagon are very close overall. what is really crazy is that the fold down seats take away over 20% of the rigidity.
anyway...i have a 2 (3) door, i like it more as most that have them do, just as the 4 door people tend to like theirs better. the biggest advantage for the 2 door is that you can hack away alot more sheet obviously. the biggest disadvantage has been so far getting out of the back when sleeping on the folded down rear seat. there needs to be an inside release on the hatch!
and if you are really worried about stiffness, build a cage!