If they replaced the sensor in the thermostat housing, they replaced the wrong sensor...it doesn't have anything to do with the light/gauge...and likely left it unplugged and/or with a poor connection. The sender for the dummy light is in the back of the head. The one in the t-stat housing is for the ECU. If that one is unplugged, the fan will run anytime the ignition is ON.
Another possibillty is that they uses the wrong sensor altogether. Then, if the ECU doesn't "see" the sensor, it will also turn the fan on constantly and the air/fuel mixture (based on the reading from the blind sensor) will be messed up. That's my take on it...I could be wrong. Don't throw this in the mechanics face, I'm not a mechanic. I'd just check it myself
Also a 96 Cherokee is NOT an FSJ.
1990 XJ Laredo - White & Chrome
1988 MJ Pioneer - Metallic Green and Black