Experienced growers don't prune lower branches. It's bad if they touch the ground, but it's better to put paper under the leaf than to cut it off. There's half a dozen or so really experienced growers I follow closely, especially Uncle Ben, and they all talk against pruning. I'm not going to second guess that much experience. But it is your plant and obviously that spot bothers you. Cut the damn thing off and live dangerously.
Happy growing.