I had kinda a similar thing happen.
I knocked out Netty early in my play through when she pipsened me and then when hostile after pickpocketing the antidote. So she attacked and eventually took spider form. I knocked her out, got the antidote and split. Later I came back and she aggroed again...this time aggroing the druids in the adjacent room...so I shut the stone door and kept my party in the lab to knock the spider out again. Well 2 of the druids from the other room stayed aggroed and came in through the door. All the others including the wolf that was in there split. I knocked Netty out again and killed the two druids who came after me from outside the lab. Once this was done I walked out of the area where the mean 2nd in charge druid ladyusually is and after loading was in the grove. All the druids were gone except for the nice one who was arguing all the time about how the 2nd in charge mean lady was too mean. He was there alone and by talking to him led me to believe that there is a story path that exists where you wipe out all the druids by killing them.
I didn't explore anywhere since this encounter but obviously something is wrong to have the whole grove population dissapear like that.
