I roll secret checks for the players secretly -- this includes many Knowledge checks, as well as Spot, Search, Disable Device, Gather Information, Bluff, Sense Motive, and so forth. Anything where they wouldn't know how well they did, and where that might be important.
Individual players in my group could handle rolling their own Sense Motive check, rolling a 2, and saying, "Oh, yeah, I TOTALLY believe him! Let's do it!" But not everybody could, so behind the screen we go.
As a GM, I could see being annoyed about swapping out a character and then swapping him back in -- if he's important to the storyline, dropping him caused problems for the GM, and then moving him back in might cause new ones. I think that it's important that you bring this up within the context of why you're doing what you did.
Good luck!