A friendly npc flew into my missile stack, causing my home nation standing to fall from over 980 to 66. This seems a bit harsh to me. Bug or feature ?

Ouch.

That sounds kinda overkill to me, faction losses for killing in npc's in hive hunt should be very low, to non existent.

Yeah it does sound like overkill. However, it's not a bug. There's currently no differentiation over when you kill an NPC, whether during a mission by accident or any other time.
If the faction loss isn't as great during the mission, how could it tell the difference between an accidental kill and a malicious kill?

If only our computers could read our minds.

As the common computer cannot, I suggest causing different faction loss based upon the sector the player is in. If it's in a/the Hive Skirmish sector, it would still cause some faction loss, but less than in a station sector? I haven't the knowledge to determine if this is workable, and if it is this still isn't a perfect solution, but it might help with the specific issue.

Maybe if it could tell the difference between being hit by a swarm that is targeted at a queen, and being hit by anything else. That would probably be fairly hard to abuse, though I don't know how easy it would be to implement.

Wouldn't help if somebody disables the AA to fire their swarms blind though.

I know this was reduced last week, but I had one question: are HS missions not in unmonitored sectors? Are npc's now treated like ctc bots? Anywhere you kill them is a faction hit? I guess that's 3 questions.

Generic convoy NPCs still behave as normal out in Greyspace, except that killing random convoy ships in station sectors hurts your faction now (that was several fixes ago I believe). Hmm, don't know if ships belonging to a different faction do that as well, I've only tried it with ships belonging to the local station.

So skirmish NPCs must be a special case.