I recall a member here had their tailpipe re-routed to prevent it from getting mangled on the trails but I don't remember exactly what he did and can't find the link.
Only way I see possible is bringing it over the frame rail -directly above where it hangs now.
Has anyone done this or something similar? Looking for 3rd gen applications only.

 

a friend from highschool redid his exhaust on a pickup similar to your 4runner. he removed the bend where the exhaust raises above the axle and then just drilled a hole in the bedside right before the rear wheel and punched it out there, looked great worked well. since you cant do that because your runner has a door there i would recomend reshaping the exhaust to just go straight back from where it bends up to clear the axle, and then drill out the rear quarter panel and put it out there.