I've never had a problem, but you should be able to take images of most fish without a flash, just turn the room lights off so it is dark and rely on the tank lights. But to get the sharpest image the best way is to use the flash and a fast shutter speed.
Using flash is fine and I will be covering it next week in Basic Photography 3. There is no issue at all as long as you don't point the camera straight at the glass, do it on an angle. I use flash for most fish photos, the fish take absolutely no notice, these below were all taken with flash, and even the Firefish didn't move, the only slight isue is with the convict who is very silvery so it blows it out a little. With the ones I took in the LFS (Convict, Freckle) the owner thought they would freak and couldn't believe the complete lack of reaction. You are better using a slow shutter speed in macro on a tripod for corals to give better colour. I think either your aperture is too low on those shots or the shutter speed is too low to compensate for your shaking. You read the Photography topic?