Keeping the truce in Sector 3 does not unlock the doors, making pacifist runs impossible.

Reported by Ezra G Melman:

3) In sector 3, if you kept the truce, the doors aren’t unlocked. This means that on hard or higher difficulty, that you can’t get past the second door outside (the one that lets you into the second building) without breaking the truce. This makes it impossible to do a full pacifist run on any difficulty level above normal.