No, it implies that they are worried about what you might say or do. And possibly not specifically you, but the odds in general of some employee or other deciding to cause a nuisance, whether or not they deserve it.
Or they have an overzealous HR person or lawyer.
Or any number of other things.
Of course they might also be a bunch of criminals, but I don't think an agreement like that implies anything in either direction.
Well they asked first so "no smoke with out fire eh" putting it in writing gives the impression that they have something to hide.
Over zealous/incompetent HR is probably the correct answer.
Seriously if you where a cop questioning some one and they blurt out I want to do a deal at the start of the interview what woudl you think
Normally in NCIS when the person getting interviewed by Jethro asks for a deal - they are the perp.
"so mr employer you admit you have done something illegal either by omission or commission and you want me to sign a compromise agreement?"
Well I am sure that my lawyers will be interested can you let me who in hr is your GC (lawyer) and I am sure we can sort something out or I will settle for 6 months right now.