There's no doubt Todd can be evil, but I think in this case it's likely that he was worried for Eileen's safety as well as his own if he didn't steer the police away from the truth. Phelan has used threats against Eileen to keep Todd quiet in the past, and he didn't have a clue about the circumstances of Michael's death or how far Phelan or Vinny would go to protect themselves.
I'm pretty sure from the way he was studying Phelan's reaction to Michael's death that he wouldn't cover for murder. Hopefully he'll do right thing eventually - but I doubt that'll be for a while since we know Phelan isn't going anywhere for the time being!