"Gel coat damage seems inevitable from tanks and weights."
Happens on any fiberglass motor craft as well. Some ways to minimize it:
Doff your tank and lead before boarding, clip it onto a line. After you board, haul them up carefully, or use the boom or a davit to hoist them aboard without having to work so hard.
Then when you drop them--don't drop them on deck. Use a rubber mat or some rubber tiling (i.e. "Dry Mat" plastic lattice deck tiles, or a rubber strip floor mat) when you put them on deck, and they should be chocked or bungeed anyway so they can't slip around.
A little work, sure, but the same think you have to do with any fiberglass boat if you don't want to chip it up. Unless you've got a bare metal work boat...dive gear is going to bang things up!