For only $9 more than the single rear window from the dealer, you can get the Bestop replacement set of all three (part number 58121-15). The Bestop replacement windows are supposed to be a near exact replacement for the factory windows and work with the factory top.
At worst, you have replacements for the side windows at almost no more out of pocket cost. OR you can sell off the side windows separately or together on eBay to another soul in the same situation you are in!
Heck, you may be able to get $50 or more for each side window--and the buyer will pay the shipping--so your net cost will be real cheap.
And be doing a public service to one or two other Jeep owners by allowing them to buy a single replacement window for less than half the dealer cost.