The correct way to do it is to have a tuning company edit the software to report all systems ready. The E39 had a common problem with the secondary air pump getting jammed with carbon. It's several thousand to fix or you could get a flash that would disable the system and report it as ready. Euro versions of the car were not equipped with the system.
'06 Arctic Metallic 325i | Sport Package | 6MT | Dinan Stage III suspension | Dinan exhaust | 330i manifold swap! Click here!
| Active Autowerke tune | 135i Brake Calipers | Deiselboost caliper brackets | E46 M3 front rotors