If you run the compressor with a bad air bag you will burn the pump out, that gets expensive. Pull the fuse until it is replaced.

Disconnect the pigtail to the compressor and you shouldn't have a problem if it does this. Also if you forgot to remove the relay and the idiot light "Air suspension" is on on the dash. Remove the battery cable again, then remove the relay while the cable is off and when you reconnect it hopefully it cleared the codes and the it is gone. I have had to do this a time or two on some till the light shut off. Also some of the hand held programmers can disable that particular code and remove the light.

Be Safe...