Been going some searching and don't see why they wouldn't install a new heater core in it for $200. They'll still most likely be making some money off of it since would say they're using new aftermarket parts.
An OE/Mopar evaporator MSRP online at Mopar-Wholesale is $309, minus $90.70 in savings, for a total of $218.30 plus shipping. And normally they're a lot cheaper than the dealer. So if the dealer is charging you $150 for the new evaporator it almost has to be aftermarket and you may want to ask.
On the same site the heater core MSRP is $150, minus $43.92 in savings, for a total of $106.08 plus shipping. Checked another site and same price. This has to be an aftermarket part, since Mopar/OE heater cores used to be about the same price as evaporators, and most likely similar to the one the dealer would install. And it isn't going to take the mechanic any full hour, at $90-$100/hour, to install the heater core in the open box.
The older our ZJ's get the more parts our outsourced by Chrysler/Jeep. Heck a few years ago the dealer installed an aftermarket/rebuilt PCM from Miami in my 96 4.0! Checked with the guy I know who runs the parts counter at the local dealer last year and he said every PCM they now sell is rebuilt.
The big difference is Chrysler stands behind their warranty on parts they sell. And that brings up another point where the dealer is going to warranty the work they do on the AC system but not sure if they would on the heater core install. But you would think they would if they purchased the part while doing the labor.
Believe it's worth a shot on approaching the dealer on them buying/installing the heater core for $200. And if it delayed getting your ZJ back a day or too later if necessary for ordering the part in it would be worth it. Good luck!