ToME: the Tales of Maj'Eyal

It's fairly clear that both the anti-magic and anti-anti-magic sides are evil, and the only way currently to succeed at the quest is to side with one or the other. Temporarily allying with the Grand Corrupter, invading Zigur, and then betraying and killing the Grand Corrupter makes a certain kind of sense, but isn't acknowledged by the quest log.

IMO, killing him after destroying Zigur wouldn't change the endgame text any, unless you killed EVERY Rhaloren elf you found, and made sure the Shaloren didn't use the absence of the Ziguranth to try to re-establish their old borders or anything like that. If you killed him and only him, then some other Rhalore elf will simply take his place. It might take an extra decade or two, but without the Ziguranth to worry about, the Rhalore will run amok; they're as zealous as the Ziguranth.

Yes, the Ziguranth are dangerous, they're zealots who scapegoat spellcasters into being responsible for everything bad that's ever happened to Maj'Eyal.
Yes, the Rhalore are dangerous, they're zealots who've been corrupted by blight and wish to corrupt everyone and everything with the blight as well.

Perhaps the "third option" wouldn't be killing him as much as it would be a dungeon that explores the lore and history of the blight, and destroying/converting the boss of the dungeon would "purify" the blight by the time you get to endgame and release the Rhalore (including the Corrupter) from their blight-induced madness. Doing the quest, as a potential reward you'd get a boost to blight and/or disease resistance. Maybe extra lore in the pride in the East that deals blight damage where they're trying to hide the fact that their powers are waning from the other prides, and the sorcerers as well. Overall idea is that it wouldn't remove the ability to do blight damage immediately, but for future generations it'd be gone; corrupters and reavers would therefore never seek to do this quest/dungeon.