Great question, and hard to answer.
Mother Nature is pretty good at keeping a balance on her stage. Some of the actors are not attractive, or even considered villains, but they have their role. Predators don't usually wipe out prey. They hunt whatever is plentiful. When there are diminishing returns on their hunting time, they move on. This leaves the desirable prey species depleted, but they can easily replenish their numbers. If predators are wiped out, prey populations can explode of course.
Even removing the muskrat could have unintended consequences, though I can't think what it may be. (maybe overgrowth of cattails and water lilies, or starving out predator species).
I think the main natural enemies of muskrats are snakes, raptors, mink, skunks, and raccoons.
We have few muskrats here, so I can't be precise. We do have lots of beaver, because their natural predators have been decimated. The result is, ponds are drained by burrowing beavers, and there is a $20 reward from the county for each beaver tail. If we had left the snakes, bobcats, and gators alone, we wouldn't be in this pickle.
Good luck with your dilemma B'ski. I know you will do what is best, because you aren't killing first and asking the questions later.
