Ah ok, that does make things clearer. I assumed that, with how the campaign has allowed the player a lot of freedom when it comes to choices, this mission would continue in that way.
I think perhaps the issue here is an absence of information that would make your intentions as a mission maker crystal clear. This is probably an extreme way to do it, but if you had the mission fail because the player left the area without the crucial information, then that would solve that problem. You get across the idea that this objective has to be completed no matter what.
Also when you present the player with an instruction to leave because of impending danger, I think a lot of players would naturally leave. At that point, when on the one hand you have objective that must be completed AND you're telling the player to leave, you're essentially giving the player mixed messages. Silly people like me

will take those instructions literally especially if they're presented with what seems to be an impossible objective at first glance.
The solution to this problem is really just to remove any information that would lead to the player thinking that they have an avenue of retreat; don't give the player that option basically. Information just needs to be a little clearer.
But now that I know that the objective must be completed, then I can proceed. Whether you decide to go in and make some adjustments to this is up to you.
EDIT: There were a lot of documents lying around so it's possible I missed them.