Unofficial Fallout 4 Patch

Does not appear that killing Dr. Chambers is a condition to end the quest as well. I just talked to her, followed the conversation tree that is supposed to turn her hostile. Then ignored her, released Amillia Stockton, talked with Honest Dan and the quest ended normally. Returned to Covenant they were hostile as per normal for this ending.

So my statement about killing her to advance the quest was in error, you don't actually have to do that. I did not test what happens if you just completely ignore her, I don't think you can get past her to release Amillia without getting engaged in conversation, but I suspect you can get past her that the quest would advance and end normally after releasing Amillia Stockton, and talking with Honest Dan. I wonder if you could get past her without engaging in conversation, release Amillia Stockton, talk with Honest Dan, then engage her in conversation what would happen?

I think the issue here is that since you can still agree with her and then kill Honest Dan for some reason disagreeing with her does not require you to kill her, and since she does not turn hostile you can just ignore her and complete the quest. Also it does not make sense that she would not be hostile when you encounter her if you already killed all the guards and are engaged in combat when you meet her. My guess is that it behaves this way in case the player character goes there first before going to Covenant to meet Honest Dan, but it would seem that a simple check for Honest Dan being a follower would have resolved that issue, in a more consistent manner. Otherwise, too me it seems that the only time she should not be immediately hostile, should be when you meet her after having been escorted by Manny or go there before going to Covenant, at least that is my 2 cents on this issue. All of which is rewriting part of the Quest which I believe is beyond the purview of this project.

I have seen her turn hostile and attack the player character if you are escorted by Manny to her, then disagree with her. The issue seems to only occur if you are hostile and have to fight your way to her location, although that may need to be validated.

So the bug is basically after you disagree with her, she should turn hostile and attack the player character, no matter how you came to her location.