Yeah, flash photog really kills color rendition. Works well to get sharp images, but most of the time the color discrepencies aren't worth it.
Only thing you can do is what you've described. Open up the shutter, up the ISO, and quicken the shutter speed. The real problem is the amount of light that gets to the sensor. Even though reef lighting seems bright to human eyes, they're really dismal compared to sunlight .... and the camera knows it. The more lights you can throw over your tank, the better your pics will be. If your camera has a noticable shutter lag, you might want to consider manually focusing to a predetermined spot and snapping the image (or a series of images) when your subject is in the vicinity. Doesn't work for fish like tangs, but is pretty effective with clowns.
