The one year I tried waterlilies, raccoons destroyed my small water garden, too. I've tabled the idea of growing expensive water plants now, but I still want the sound of moving water, feeder fish and a spot for small critters to drink where I can watch them. I wouldn't enjoy it if it were covered with wire or other man-made stuff, so instead I covered almost all of the open surface with large (and heavy) flat rock. Bricks inside the pond support the flat rock which sets on top of them. Having the flat rocks suspended over most of the surface combined with spaces between the supporting bricks offers fish many safe hiding places from predators, plus the fish are not as noticeable; mine, for instance, are only readily apparent at scheduled feeding times (which are never late in the evening).
I guess waterlilies wouldn't work in this because there's not enough surface area exposed, but maybe they could be in a fish-free pond? Then, maybe you could occasionally exchange water back and forth between them, pleasing all the inhabitants?
Here's a few ideas.
The year after the major raccoon attack I covered even more of the water surface with rock, but I'm not finding pictures of it right now.
