I think that I would have followed Chakotay's example in this case.
He was a good leader, and his people were loyal to him; but I admit, I am somewhat surprised they made good crew. The ordeal with Seska also may have been sobering for some of them.
I agree. I think that Chakotay's influence in this matter helped a lot to intergrate the Maquis into the Starfleet system on the ship.
I also think that Chakotay was smart enough to pick the right people for his Maquis crew when they were still fighting the Cardassians, with a few exceptions: Seska, Suder, Jonas (and Paul Fairman who is a character in the book "Incident At Arbuk").