Detection:
http://forums.insideqc.com/viewtopic.php?f=12&t=5835
And in hardware-accelerated engines it should be easy to combine warped textures with non-warped lighting through shaders.
This doesn't need shaders; hardware-accelerated Quake already uses two separate sets of texture coords for difuse and lightmap, so just warp the diffuse coords only but don't warp the lightmap coords.
The issue is that whatever way you slice it, it looks bad.
I do understand where the desire to do this comes from. You've built a map, you have a large water surface in it, the surrounding geometry is nicely lit and shadowed, and the fullbright water looks bad. And you're right, the fullbright water does look bad, but lit water actually looks worse.
The two big problems are (1) when the lighting on the water is sufficiently dark you can't see the warp effect at all i it just looks like a big dark spot, and (2) with translucent water enabled the water just disappears.
This is an example of taking a special case and wanting a general case solution for it, but not properly considering how that general case solution may or may not work outside of the original special case.
"Can I have lit water?" seems a reasonable request, but you also need to be thinking about lit laval, lit slime, lit teleports, how it interacts with translucent water, etc.