I have, on occasion, left flies in a musky's mouth when fishing alone. Some times landing the fish, dealing with tools, and unhooking the fish solo is too much and cutting off the fly is the easiest route.
I got curious about it and contacted the WIDNR musky manager as to what is the right thing to do and he said:
I think you did the right thing with that deep-hooked fish. In most cases, that hook will work its way out. That fish's chances are probably better than if you had worked long and hard to try to remove the hook, especially with the fish out of water in the heat. Any time we have fishing, catch and release or otherwise, some fish are going to die. We try to take that into account in our management.
Tim Simonson, CFP
Bureau of Fisheries Management
PO BOX 7921, 101 S Webster Street
Madison, WI 53707
As for this comment:
Crick Addict wrote:
It's only a fish for dogsakes. It's not like a child or a baby kid... 
These are not trout and there are not billions of them per mile. Vito makes a good point - but he does sound like a wiener calling me irresponsible for using fluoro instead of wire.