You should be able to eliminate the the BCM (with a lot of work) on any Cobalt but the LNF. You still have to get all of the lighting worked out, but the Anti-theft stuff can be turned of for the ECM with HPT. The LNF/Turbo\/E69 is a little trickier since HPT can't disable the anti-theft. There are post on HPT claiming they worked around it, but none that really explain how. Here is one that explains how for a GXP but his explanation doesn't exactly match my understanding of the LNF Cobalt system.
LNF standalone ECU options? (hptuners.com)
LNF standalone ECU options? (hptuners.com)