Wanting to machine gun Mary Jane and Aunt May would be a dark desire. Wanting to marry Gwen, not so much.
I think his actual deepest desire was to have saved Uncle Ben and Gwen. Marrying Gwen is just the way things would have worked out if they hadn't died. Actually, if his deepest desire is just to have saved Ben, that probably would have been enough of a change that Gwen wouldn't have died.