I am guessing you are talking about a soft top.
I pull all the soft top rear windows out quite often in the summer and run it in "safari" style.
You probably can drive around with the back window in, but I would just do it around town, and not do highway speeds, but you may be fine regardless.
What I wouldn't do, is just remove the rear window and leave the rest, at least on my TJ if I do this I get quite a bit of exhaust into the cab. I got my JK later and just never tried it.