That is a totally understandable and justifiable concern, and Sweets looks appropriately horrified as a result. He knows that every agency has it's dark side, but there's something about the CDC that is supposed to protect them.

"What? That's ... do you want me to call Agent Booth? See what the FBI knows?"

He knows that the government isn't always trustworthy, but Lance trusts Seeley. He knows that Agent Booth is one of the good ones, and he'll be able to help - or at least try.