Being involved in an off-duty shooting wasn't so bad, after all the wounded guy was fleeing a felony, failed to stop when Munch yelled "Stop Police!", and took a couple of shots at John.
No, the trouble was, Alyssa, being an M.E., came out to check on the guy, and she didn't bring the room key. So, here John sat in just his pants, while Olivia and Elliot came to investigate the rape-homicide the guy had committed, and a couple of suits from IAB came to grill him about the officer-involved shooting.
Next time, if there was a next time, it was definitely his place.