Besides, I get most satisfaction by winning the game without injuring any of the NPCs. I have a personal dislike of using Armageddon on an area containing NPCs which have not attacked any of my party. But that is my personal preference.

However, IMO the key argument against your suggestion is that you can at any stage of the game gain a notorious reputation by selling the bones from Bootleg Bay (it respawns fairly quickly), and getting your party healed by the Curator in Castle Kriegspire. In contrast, once the quests that raise your reputation are done, there is no legitimate way of gaining a saintly rep. None. No way - end - finito.

There are enough "good" quests to enable your party to do things in the way you suggest, but I submit that it is not at all the preferred way of doing things. Your way would be even less preferred if the game did not contain the option of donating at a "good" temple to get your rep back to honourable relatively painlessly.