I thought part of the problem with "The Disease" was that Harry had caught something due to his liaison, and this "sexual prime directive" thing was just a joke about proper quarantine and medical procedures when dealing with a new species. Namely, you don't pork a new species until you know what you can get when dealing with them (and Kirk probably had been the precedent set for why we don't do this).
Pretty sure no. Were Paramount do a new series set in that time period, they could ignore it at will (they might mine it for ideas, though). Though what is this doing in the Star Trek Voyager Wallbangers section, I have no idea.