To be clear, Pres. Obama said he had confidence in the SS, not that he had confidence in who was running it. So, what I gathered from that is the President is trying to reassure the country that he still firmly believes that the agency whose job it is to protect himself and his family is still very capable of doing that job. To say otherwise would not only enlarge the shadow of doubt that already looms large of the department but may also invite others to try to breech SS security because they just heard the POTUS say he no longer felt the agency capable of doing its job. That's certainly not an impression you want to give.
So, but him saying he still had confidence in the SS but accepting the Director's resignation is sorta the "damned if you do, damned if you don't" type of scenario. If he had said anything to suggest he didn't feel safe with this agency guarding him, can you imagine the fallout? We're talking a complete overhaul of the SS, not just replacing a Department Head or changing some security procedures/protocols.