I can't speak to President Roslin's motivations. I do know that, with the responsibility for the lives of the rest of the human race on her shoulders, she almost never has the luxury of choosing between a clear good and a clear evil.

His eyes darken as he considers ... and remembers.

You know that, not long before Hera's death was faked, we had to deal with a hostage situation shortly after the fleet learned of your existence. We lost lives rather than hand you over to terrorists. It was only a matter of time before the fleet--and any Cylons planted in the fleet--learned about your daughter.

I suspect that President Roslin believed that secrecy was the best way to keep Hera out of the hands of both the Cylons and vengeful humans, without risking more lives.

I don't say that I agree with her decision, but I do believe she was trying to do the right thing. Or at least a right thing.