It's not the end of the world to run without the rear sway bar the newer SE TJ's don't have one. However there is no real benefit in removing or disconnecting it either, the rear flexes fine with it hooked up and it does help to keep it from leaning over on of camber sections, also help eliminate a bit of body roll on the street and it helps keep the rear springs in place offroad.
See plenty of flex with the rear swaybar hooked up and the front anti rock swaybar hooked up also