Fixed for the next patch. Did some testing with your saves and things seem to be behaving as they should. So, persuading the mindreader to let Buzzer live will no longer affect the player's score in DC negatively, and those who did just that need not worry as long as they haven't talked to the Faceless commander yet. Those of you who avoided talking to him can do so after the patch rolls out.
However, this bug could've also prevented some of you from even being allowed to enter the Faceless territory, as the two checkpoints are where the Faceless check whether the player has helped them in either RC or Foundry; those who did only RC, and resolved it by using persuasion, were most likely forbidden from passing through due to this bug. Sadly, there is no way to redo any of these failed checks.
Thanks for the saves (and the patience), and sorry about this nasty "feature."