Yes, RE is pretty expensive. I haven't personally tried Rusty's suspension, all I have from them is a trackbar but I believe they'll be the best bang for the buck, unless you want to try Rough Country.
Their 4.5" Spring Over kit is $550 including their shocks and I believe has everything you need, though you'll need to weld the spring perches or just replace the rear end with one out of an XJ. The jump to a long-arm suspension goes up to $1600 for a 6.5" kit.
Personally to me, if I had an MJ (and I want one bad), I'd piece together a kit. Replace the rear end if it isn't that great with one out of an XJ, otherwise put new perches on. Put an AAL in the rear and maybe a shackle too unless the springs are shot, then just replace. Buy 6.5"-up coils, and a long-arm system. Then buy shocks and whatever else is needed, if I swapped rear ends perhaps sell the old rear end to make a little money back.