Not necessarily. The factory a/c setup does use the PCM to confirm the hi & lo pressure switches are closed (the system has pressure within the acceptable range) & also to slightly raise the idle speed to compensate for the increased load from the compressor.
Depending your actual new setup it should be easy to work around the PCM with a slight wiring modification while still having the pressure switches functioning as they do now. As for the idle adjustment I would say with the added power from your LS you will not have a noticeable drop in idle speed so not to worry about that.
All you should have to do is run the compressor feed wire from the mode switch to the compressor relay rather than to the PCM. Somewhere along that wire is a splice with one going to the PCM & the other going through the hi & lo switches then to the PCM. You need to get the one from the switches to the PCM & run that to the relay. That is a grounding wire so when you switch the a/c on it will then be used to ground the relay coil wire to close the relay (if both switches are closed) & engage the compressor.
The wire color & routing may be dependent on what year TJ you have.
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