I finally got through Forging the Pact on my 5th attempt. What I noticed that was different this time is that Trahearne had dialogue when we got to the first group of researchers, which he had never said before on any of my previous attempts. This suggests the problem might lie with Trahearne’s and other NPCs’ dialogue scripting, and can be used as an indicator of potential future problems when doing the mission — i.e. if he doesn’t give a little speech when you get to the lab at the top of the hill and defend the researchers there, you may as well not continue into the cave because it’s going to get blocked.
The only thing I can think of that I did differently was to (a) fight my way all the way to the researchers rather than running partway through the mission to speed things up, and (b) don’t rush ahead when you get to the barricades on the hill, but try to kill anything coming up the hill before you go talk to the researchers.
In general, you can’t rush through ANYTHING in this mission or the dialogue will get messed up, but must go slowly. (In contrast to many other personal story missions where it seems rushing through and ignoring monsters is the only way to get anything done, due to endless respawns. Ironically this mission has endless respawns too, so you’d best bring have enough firepower to kill stuff reasonably quickly.)