The air pump is "deleted" if you just unplug it. I removed all of the equipment on my SS, though, much more space. The tube that goes across the front is just about impossible to remove in one piece. Just cut it under the balancer and take it out in two pieces.. No AC removal needed. Don't forget the plugs for the manifolds.
Yes, you need it programmed. Unfortunately, the codes you now have have nothing to do with the air pump. I think you've unplugged the crankshaft position sensor from the timing cover.