that's horrible. i understand why that happened, because that can be the case in many ways, where locking an alter up can make them feel even more like a monster, more unloved and more resentful, but that is not the case every single time, and it takes careful assessment of the situation to figure out what may be the best approach. with an alter that is actively trying to hurt the body or even kill it, i would say that is the best approach at the time.
i'm sorry that happened to you. you are not abusive for that. especially since you are now on much better terms with lily, and surely giving her the support she needs to thrive.