Ehhh I disagree, the slavery bit is almost entirely dropped after the first chapters. It's mainly used to represent just how much Chise loathed herself and Elias' lack of human understanding, both of which are then the main character developments of the series. It's meant to be the lowest point for both characters that they then get out of through the relationships they build, not just with each other (some early chapters make it clear that the two alone is an unhealthy relationship that will probably kill Chise) but also with their friends.

Admittedly this reading is only made clear at the end of the first arc though, and I can vaguely see how you might get a fetishy reading from it (in the sense of slavery leading to her being "fixed," since that's a huge ick). But I still don't think it's nearly close to the same level as Shield Hero outright arguing slavery is perfectly fine if you're in a pro-slavery world and the person consents.