Necromancer has chapters and it's one of the most cherished storygames on the site, so there's clearly nothing wrong with marking a major event as the turning of a chapter. This works because the storyline is big enough to affect the setting and characters whenever it evolves.
Zake, I think you have given some of the best writing advice to ever grace this site. Thanks so much.
This is fine. I would, however, suggest including some important decisions before the last chapter (this includes ways to end the game) because it would be a bit too linear to have 90% of the story not affecting the outcome.