Yeah, that stood out to me too. I suppose that's the legalistic caveats she would've had to say. I can imagine that type of thing being said in the real world. I really wanted her to say, "I'll have Book take you both to the Gamma Quadrant Colony!" Although I can't remember if Moll mentioned that to them or not.Also can I just say, Burnham is really terrible at talking down people.
She could have easily said "Give it to us an we'll put you in the Federation version of witness protection".
But no, instead she was all "You have to go to jail for these unspecified crimes! But if you stop struggling I'll recommend you're put together!". (I say unspecified crimes because the only crime the two have actually committed against the Federation is the time bug that did absolutely no damage to anything.)