Maybe you could build a canopy over it. With some Metal Halide's and VHO's to supplement........... ok sorry. Getting a little ahead of myself here.
I dont have any experience in ponds, but i do see how that darn tree could be a problem. Would cutting a few branches work? But then you have to deal with the wind blowing them anyway... HMMM theres gotta be a good solution to this. Is moving the pond even a thought?
Climb on in every so often and get them out with your hands. Thats what I do but watch out for snakes and frogs. Frogs are almost worse than snakes because when you step on one of the slimy guys at the bottom you think you've stepped on a snake.