Indeed, it is uncomfortable. It's supposed to be.
Jorou is self-harming, overworking and starving herself, and lashing out at others. The people close to her don't know what's going on with her, let alone how to help her.
Medication, counseling, and monitoring her condition? ("enslaved" as you put it)
Or to ignore her violent outburst and self-harm and just act like nothing happened?
They don't know the right answer. It's not a situation Sable or any of the main cast are equipped to deal with, nor do they grasp the depth of why she's acting this way.
I should point out that there is a third ending for Jorou. It was added in version 1.04.
It doesn't conclude the matter of her self identity, however. It's only in the Joanne ending that Sable really learns about that.
The third ending sets up the transition into Sable's Grimoire 2. That's where Jorou's route will continue (rather than as a separate game like for Lisha and Drakan) and her self-image will come up as part of her route, rather than just as an ending.