I've run in to it. I do find myself getting attached to my faction so to speak. I play on a PVE server and during the Rak Event this really came to the forefront. Me and some guildies would be running through the dailies and run into Imps. Now, I'm not one to start anything really. I don't PvP much as a matter of preference. But sure enough 1 or 2 of my guildies would be flagged and bam! they would get jumped. Now fair is fair, the guildies were flagged so no faulting the Imps there, but my reaction was scary. lol. I would jump right in there and we would go at it until they wanted no more. If I died, I was doubly determined to get back in there and get my revenge. It was fun.
I found myself very protective of my guildies which I guess is natural. But the next night... I was looking for the purps. I flagged myself and was just waiting for the slightest flinch.
Now... when I see what you have described happening with NPCs, my immediate reaction is to see if they are flagged for pvp. If so... I jump right in there an defend my crew.