I think it looks great.
I stained and varnished my benches (some of them were new butcher block, one was an old solid-core door, the rest were in-between) and I got hit with the same dilemma. If it looks nice, you worry about working on it -- which is crazy.
I put some rubber mat on mine -- but it's really there for dripping liquids more than preserving the stain and varnish. If my workbench looks like a dining room table, it's a good sign that I'm doing something wrong. I think the scratches and dents will continue to add character.