My point was killing the undead would not be "killing" the original creature, since it already died some time ago.
Yes, this is actually the reasoning I am using to avoid having to completely change the game around for chapters 3 and 6.
I have finished going through the game and finding all the places in the main line quest where the party is forced to make a kill unnecessary to the plot in order to proceed and have drafted an annotation of what needs changing with some suggestions for how to change it, as Berelinde suggested. Here is what I came up with:
Baldur's Gate II - SoA Pacifist Mod
Concept: To permit a player to complete the MAIN LINE of quests without also REQUIRING any kills except Irenicus (and assorted already-dead vampires, including Bodhi).
What this mod is not: This is not a mod to tame everything in the game. Monsters will still attack you. You are free to strike back or turn the other cheek (or run past them if you can). All this mod provides is an unlocked door at the other end if you choose to run.
What this mod is ALSO not: This is not a moral judgment on how to play the game with a good alignment. Not killing an evil creature can doom a good one. This mod simply provides the player with more roleplaying choices than he/she previously had.
Solutions (by chapter):
Chapter 1:
Required kills: 4 mephit portals (AR0603).
Description: the door leading to the exit remains locked until all the mephit portals are dead.
Solution: Door is always unlocked (Why is it locked anyway? Did Yoshimo lock it up?)
Comment: Yes, the mephit portals will continue to spit out mephits. The only change is that the player is not REQUIRED to kill them to exit the dungeon. He/she can run instead.
Chapter 2:
No changes required.
Chapter 3:
Required kills: Jaylos, Caehan, and Gracen (the defecting thieves and their contact at the Five Flagons Inn AR0511).
Description: Female PCs are required to kill all three men (and male PCs might be required to do so as well, since the only existing journal entry for the quest states they are all dead).
Solution: Change the dialogue so there is an option for the player to actually fool them into believing the party members are also defectors (this dialogue is already written).
Comment: While several vampires get staked in this chapter, being vampires, they were already dead, so no changes need to be made to the remainder of the quests.
Chapter 4:
Required kills: kobolds (AR1507), myconids (AR1503), and a troll (AR1506).
Description: "Graduation" from Spellhold requires the party be put through a series of tests. The first two of these tests require the party to kill everything in sight before they are permitted to progress (and progression is only via teleportation). A subsequent test requires a troll to be killed for his head, whether the party wants the treasure the head will grant or not. This later room is already set up so that it appears to have a door that will not unlock until the troll is dead (I know it's a teleport too, but it looks like a door because it is around a corner).
Preferred Solution (for AR1507 and AR1503): Provide a physical exit from AR1507 and AR1509 opposed to waiting for teleportation. Allow the party to either kill the monsters (as in vanilla) or run past them to the exit. The keeper mage can meet them there and say his lines, similarly to the way he meets them in the troll scene.
Alternate Solution (for AR1507 and AR1503): Allow the keeper mage to permit progression (via teleport) from AR1507 and AR1509 if the party can render either a) the kobolds and myconids neutralized (via sleep, confusion, horror, etc., or anything else that disrupts them without killing) or b) the party inaccessible to the monsters (i.e. invisibility, protection from weapons, etc.)
OR: If the game can detect that the party did not kill any of the kobolds in AR1507, transport the party directly to AR1506 (this implementation will not require any changes to AR1503). Reason: the keeper tells the party he doesn't know why they ended up in AR1503; that it must have been some sort of setback. This solution gives context to the setback.
Solution (for AR1506): Change exit door (or teleport) from AR1506 so that it is always unlocked (or attended by the keeper mage). Reaching the door will permit the party to progress without needing to first kill the troll.
Comment: The kobolds, myconids, and trolls will not go away and will still attack as they currently do. The only difference is that the player will not be stuck on that scene until the monsters are all dead.
Chapter 5:
Required kill: Demon in svirfneblin city (or the svirfneblin leader).
Description: The party cannot exit the Underdark without first being disguised as Drow, or without killing the Drow party that guards the exit. To be disguised as Drow, the party must meet Adalon, but they cannot get the gem that permits access to Adalon until they first kill either a demon or the svirfneblin leader. (While a thief could pickpocket the gem, not all parties will have this skill).
Solution: Alter the dialogue with the svirfneblin leader in AR2100 so it is clear that the demon can't really be killed, but just banished to its original location (plane?) and the "doorway" to the prime material plane locked with the earth scroll the svirfneblin provide. I know this may be obvious already to many people, but it needs to be said more explicitly.
Comment: I will write the dialogue changes for the party interaction with the svirfneblin leader.
Chapter 6:
No changes required.
Chapter 7:
No changes required.
I do need help to make this a reality. I'm a dialogue writer; I don't do much else. Thank you to everyone who has commented on this subject so far; I really appreciate the interest.