You're making it sound like that's escaped me, and it hasn't.
I'm sorry but by your post is painfully obvious that it has.
You are oversimplifying one of the manifestations of this freedom as "killing everybody without rhyme or reason " and it goes beyond that, freedom implies divers ways to approach a quest apart from clicking everyone until they stop moving..
I can only assure you that it hasn't. As far as "freedoms" (in regards to this particular topic) go, I believe we can summarize them as:
1) Multiple ways to advance a quest, which includes makings sure there isn't a set order in which to approach a quest.
2) The ability to kill any NPC without breaking the game.
Of the two, the latter has the most significant impact on production. The two are certainly linked, but the latter extends beyond the first in other ways. Are you seeing anything beyond those which I'm missing? If not, then I'm not oversimplifying it (although I do try and describe them in ways that are simple just for the benefit of the post).
And before they're mentioned, while mechanics like a classless design and a variety of skills and talents to choose from are certainly another form of freedom, they're not relevant to this specific topic.
You said..
..factors like spells, information gathered, factions, previous quest results and a lot of other things that aren't just an alive/dead check are going to make the implementation of elaborate schedules hard.
..and these are all factors that another game with day & night schedules had to deal with (Skyrim). However, Bethesda prevented many problems by not allowing players to kill critical NPCs. This is something Divinity intentionally allows other players to do (despite the number of issues it causes), all in the name of freedom. And if it's an option you appreciate having, then great. For those of us that don't walk into virtual towns with the intentional of killing NPCs for giggles.. meh. I would have preferred less work on this front and more time spent on day & night scheduling instead.
In the end, a feature that only a portion of the playerbase will appreciate having has caused enough design headaches that we've lost a feature that would have impacted the entire playerbase. To me, that was a bad tradeoff. Day & night schedules would have had an impact on the gameplay of everyone, period. On the other hand, you could remove a significant portion of the freedoms we're discussing in this thread and players like myself wouldn't even notice.
Unfortunately, we are long past a point where anything can be done about that now (beyond expressing our disappointment or otherwise). But even that can be useful if it's kept in mind for the next game and/or future updates to this one.