PCM/ECMs rarely go bad, however they do once in a while kick the bucket. I would venture to say most of them are replaced due to poor diagnostic abilities, only a portion of the ones replaced are really bad.
That said, a good shop should be able to easily pinpoint the cause of your misfire. They should verify there is power to the ignition coil, and that the pcm can ground and unground it causing it to spark, and there should be power to the injector, and that the pcm is grounding the injector to make it spray fuel. If those things are good, then they should make sure that the injector and coil works properly, the plug is good, there is compression and valvetrain is sound. However if there is an issue with the pcm controlling the coil or injector, they should check for operation at the pcm connector. If that checks fine, the pcm isn't your problem, its wiring or a connector. If you still have an issue at the pcm, then the proper thing to do before condemning the module is scope the cam and crank sensors, make sure their patterns are correct and in synch. 1-2 hours to verify this. Whether they actually do this or not, is another story. There was a horror story on the jeep kj page on facebook recently of a shop throwing everything at it when they thought it was a similar issue. Turned out to be a loose valve seat.