You don't have to doit, but
You can buy a "flashpac" module that will reset your ECM and other things, but I don't know about those ($100/200 bucks)
You don't say, but your JK has to me a late '07, or newer !!
If you just replace the "sensor" with a rubber valve stem, then you will always "alert" the TPMS system and there will be a little "chime" when you first insert the key and a little Tire profile light on the dash
If you can live with that--use a rubber tire valve stem and tell the shop TO REPLACE YOUR VALVE STEM WITH WHAT YOU SAY !!!