Brett, you and Donna have built an amazing place. I think you have no choice but to protect the integrity of the pond. Perhaps the muskrats can be a part of the scene by putting sparce "Natural" riprap that holds down chicken wire around the pond banks you prefer left alone. Your stand of native grasses will completely cover it soon enough. It could be a great compormise.
I also liked that your trapper ASKED if he could do more and graciously accepted you denial. IME, People that ask are rarely a poaching/trespassing concern.