The SEC's basically acting as an enforcement body and a standards organization in this case. Lying to them allowed Madoff to perpetuate his fraud, and perhaps more importantly to legitimize it; he wouldn't likely have been able to manage billions of dollars if he'd been operating outside the regulatory framework. I'm not sure I'd call that intrinsically immoral, even with my deontology emulator on, but in this context I think I'd be comfortable saying that it acted to exacerbate the situation.

It looks like he'd tried to stay out of their sights as much as possible, though. Judging from Wikipedia, most of the investigation here was carried out by his competitors.