I've been doing combat bonds and warzone BB missions in Banki since the community goal started. I've been fighting for the Banki Gold Gang the entire time. I take several BB warzone missions at once and head out to the war zone. Sometimes I'll even come in a bit early (for example, you need 9 kills but only get 5) to refuel and rearm and pickup another few missions or so before heading back out and completing the mission(s).
So far, they've all completed successfully for me and have added rep appropriately. I only take BB missions assigned from the side I'm fighting for (or ones that are Neutral such as the Banki Union). I'm allied with the Banki Gold Gang, friendly with the Banki Union, friendly with the Feds, and neutral with the Banki Advanced Gold or whatever the other opposing faction is.
From what I'm reading, experiences seem to differ here so I figured I'd add my own experiences. Or maybe I'm missing the point of the post?
Edit: Avoiding a double post, I have seen a few instances where I did significant hull damage to a ship that an NPC was firing on, didn't kill it (the NPC did), but didn't get the credit for the kill. On other instances, I've done a small amount of hull damage to a ship and an NPC killed it 10 seconds later and I GOT the credit for it. So maybe that's a bug?