You can buff out the scratches without draining the tank. You can use micromesh sandpaper (the kits I've used go up to 12,000), although I've never tried to do this on a running tank, it can be done.
Your best bet is to obviously try to avoid scratches in the first place. I've always avoided sand substrate in acrylic tanks (even though it looks awesome). I've always felt it was too risky to get some sand caught while you clean algae off the walls. It's also good to go with thicker acrylic. It's a lot easer to scratch a panel that has a lot of deflection than one that is flat.