I wasn't answering a question about the magisters; I was answering whether killing them in this circumstance would be counted as taking an innocent life for the purposes of a later quest.
Loading a save in the editor, it should be possible to check the flag used for that quest, to test whether certain actions are counted for this purpose, or not.
In the editor the command "oe PoB_CheckFlags" should list debug text checks above all player characters' heads.
One of the programmers checked recently when someone asked about the Path of Blood trial / Puritan's Walk achievement, and provided a list of most of the actions that would affect this (he wasn't able to look up a couple of things).
For the purposes of this trial, the flag used is named GLO_PathOfBlood_MurderedInnocent.
What counts:
0) killing any character in the game, except for the tentacles in the Arx harbour (using a summon to kill someone is fine though)
1) releasing death fog in Arx
2) snuffing candles during the Doctor's Weakining ritual in Arx (and completing the the Weakening also marks Lohse as having killed an innocent)
3) giving a dagger to some Black Ring in a dialog on the Nameless Isle
4) allow companion Ifan to kill Saheila in Fort Joy
5) allow companion Ifan to kill Alexandar in the Nameless Isle
6) allow companion Sebille to kill Stingtail in Fort Joy
7) killing Jonathan (in dialog) in Reaper's Coast
8) killing the source lich (in dialog) in Reaper's Coast
9) killing Lohar (in dialog) when he begs for mercy after beating him (I think that only happens when Ifan companion is nearby)
10) killing Mordus (in dialog) after he begs for mercy
11) killing Owin (in dialog) near the oil fields in Reaper's Coast (the execution scene)
12) something in the ARX_Cathedral_DivineTomb_PoB_LucianStatue.lsj dialog (no idea what)
13) something in the CoS_Temples_Human_BlackRing_003.lsj dialog (no idea what)
