I've got at least a few former sage citizens, in fact (most of the naturalized citizens used to be performers).
Bedrooms for residents should be hooked up to the tavern: if hooked up to the library or temple they won't work, I think (there are reports on the forum. I don't remember if those bedrooms were claimed by citizens instead, but they didn't work as bedrooms for residents tied to libraries [and there aren't any tied to temples yet], and your experience confirms that).
I doubt assigning bedrooms to libraries will break them: the museum breakage was essentially caused by the museum usurping the library rather than enhancing it. When I moved the museum link to the tavern it worked a bit better in that socializing is performed in both places, but no instruments were moved to the tavern (or, indeed, at all) until I installed chests in the library, at which time instruments were moved there. As I don't employ poisoners in my tavern I don't know what would happen with goblets or if a museum would block poisoning activities.
The scribe option is indeed how many copies of each original you want. However, I don't care about copying. Visiting scholars steal books, but they also write books (assuming it isn't stalled), and the thieving/infiltrating artifact seekers frequently carry lots of books that I have to take care of once they've been put down. When I last checked, I had over 500 books.