Let’s face it. It is a bit of karmic justice that Illya is the one who ends up with her soul stuffed in a doll. Fate/Stay Night Illya loved to throw people’s souls in various objects. Most of the time Shiro winds up with his soul smooshed into some doll if he gets captured by the Einzbern’s White Holy Grail. Mind you she also saves Shiro’s life with the same technique at the end of Heaven’s Feel but that is only when she is on her way out while being consumed by the Dress of Heaven. Illya’s always a little nicer when she is second away from death. There is a reason Fate/Stay Night’s Illya’s wresting name is Cutie Heel Bloomer.
Now magical girl Illya is a far kinder version of the character whose general methodology would not casually play with people’s essences for fun and profit. But much like Karna, she has to pay for the crimes of past lives despite the fact that she had done little to deserve such punishment in this timeline.