So for some reason in spite of doing everything the right way in this quest; that is creating the power armor using Gold and Lithium, then talking to Molly who took me to the director and killed him, this quest is marked as failed in my pip boy.

I didn't do the optional part that suggested I find an alternative way of escaping as I know that turns the bots and turrets hostile.

That is the alternative.
Molly gets killed in it too.

Well, you have to kill her if you use the alternative method to escape.