Somehow could maybe work modulated / multiply blending on it instead. You can do this in Darkplaces by having a q3 shader script for that, and engoo (SORRY ABOUT THIS SELF PROMOTION

) also has an option for multiply water, which gets along better in dark areas at certain water alphas. Quake 3 used multiply water a lot BTW, mostly without lightmaps as well even though water can have lightmaps in that game.
from the beginning water can't have lightmaps because their surface was always rendered with turbulence which uses different span code, it doesn't even have mipmaps