I honestly think his Jekyll/Hyde personality is still relevant to his character and that he will come back, and maybe not as a villain.

I like the idea that his regular side (Jekyll) may have been unaware of all the horrible shit going on and that he genuinely had feelings for Wednesday and didn't think too deep about helping her, but when Thornhill was controlling him it brought out a different personality to him (Hyde) that wasn't just the monster.

I'm kind of hoping that's what they'll do next season. I really liked his character and would love to see the Jekyll/Hyde outcast welcomed back to Nevermore in some way, even if it's on the wrong foot.