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Once I heard someone said that there's no such thing as bad publicity. I think it could as well relate to your situation there: you have a great character to begin with and a vocal audience that "wants her back". In my opinion, that's a win. 

Her turn to a darker self is effective **because** your audience loved as she was before, thus there is dramatic tension between past and present. No mistake done there - you can go give yourself a pat on the back.

Regarding the future of your story, you should do as you want. Having close-knitted, small audience is great, but you shouldn't get caught in a feedback loop. Writing is up to you. 
Audiences are entitled to their interpretations (and of course, opinions) on a story, but they won't write for you; trying to please them might as well be like chasing rainbows.

Write the arc you want to write and makes the most sense in your mind. If you do a good job they might disagree, but they'll follow along.