Did Shouko kill people to make the Setsugetsuka dolls? It's hinted that in order to make a banned doll, you have to use human parts. In the manga, Charlotte is struck with how much bio parts Yaya has.

Did Shouko actually kill people to make the Setsugetsuka dolls?
Yes, she did (Yaya is a banned doll, as Charlotte discovers Manga, anime). Banned Dolls are created using living parts or a whole living organism, human or otherwise (like Frey's dogs). The best banned dolls use human parts, and the machine dolls (Yaya supposedly is one) are made from living humans altogether.

Anime episode 12, talk between Magnus and the teacher.

Shouko is shown in a flashback bargaining for Raishin's body (part of the reason she left Yaya with him to begin with) so she could make more automata also episode 12.

So all Magnus' dolls, Elf Speeder's butler ep12, Setsugestuka, and probably cannibal candyshe could use magic independently inside the vault. were once living people (or parts of) turned into automata. 

Let's not even go into the ethics discussion... XD