Well, I checked the FS Wiki and it appears that the Myrmidon is the ONLY fighter in the GTVA that doesn't carry the Harpoon. It is a bit strange, won't you admit ? Then again, it is one of only four fighters (the others being Perseus, Seth and Tauret) that can carry the Stiletto II.
Then I looked at the GTM Harpoon entry. "The GTM-19 Harpoon is one of the newest missiles in the GTVA tactical arsenal." is what we can read in the intro. Since it's not from the Tech Room, I assume it's not a canon information. However, given that we know for sure that it is "the most sophisticated weapon in the GTVA arsenal", we can safely assume that it was developed in the recent past (several months, perhaps a couple of years before the Second Shivan Incursion). Who knows, maybe it was a response to the NTF Rebellion ?
Now, it's me speculating, but is it THAT improbable that the Harpoon was introduced after the Myrmidon ? That would explain why there was no initial compatibility. Now, why wasn't it refitted ? Who knows. Perhaps the "ultra-efficient hull configuration [that] provides space for three secondary weapon systems, a first for Terran-Vasudan fighters" thing prevented them from it ? Or perhaps the Myrmidon is supposed to rely primarily on primaries for dogfighting, thus making such a refit too costly and not effective enough in the eyes of the command ?
After all, it does have 6 guns - that's equal to the GTF Hercules, GTF Ares, GVF Tauret and second only to GTF Erinyes. All of those are so called heavy or assault fighters. Now, in-universe at least, a space superiority fighter with the primaries of an assault one surely is supposed to rely on its primaries, with the secondaries being reserved for more specialised or support tasks. Think Erinyes, but to a smaller extent.