Harpoons are far and away the most popular and powerful missile, and while there may be some disagreement about whether or not they are too good, there is no argument that they aren't very good.
Would changing the Harpooned condition card to only affect large ships help bring them back into line a bit? It makes them a bit more thematic (they punch through smaller ships and cannot embed in them) and a bit less powerful. It would certainly take their boot off of the neck of swarm lists, but would it be enough to ease them back from being the only missile choice, to just a great missile choice?