There's no real way of fixing it I don't think.
I've tried running with 4x4 supersampling and 16x AF and I still get shimmering.
The 4x4 supersampling means the image is rendered at 4 times the display resolution vertically and horizontally, then the end pixels are sampled from 16 pixels of the super-high-res image. This gives perfect image quality, but the worst performance in the world.
My point is, even with that, I still get shimmering.
What you could try doing is finding replacement water textures that are lower-resolution than default, which'll make closer up water more blurry, but distant water less shimmery.
Additionally I've always thought of decreasing mip-map resolution by twice the amount than normal, but I don't think anyone's tried that, and I myself don't intend to.
The next FSWC, however, has some, actually quite a few, modifications that modify the sun's reflection on the surface according to altitude, and from the screenies I've seen this new feature we're adding could possibly help decrease shimmering, but probably not solve it.
It's a bit of a shame, but who knows, maybe we'll work out something in the shader that'll be like a magic cure

.