Unfortunately, the problem that existed at the beginning of "Malignant" still remains: since Gabriel and Madison share a brain, there is no way to completely remove Gabriel without killing Madison. Therefore, although Madison can trap him — as she successfully did for most of her life, prior to the events of the film — she can't get rid of him entirely. He's always there, occupying some part of her brain. She even acknowledges this in the end, when Gabriel taunts her that she won't be able to keep him locked up forever, and she agrees.
However, this time Madison is an adult, not a child, and has no intention of burying what she knows deep in her subconscious again. This time, she tells Gabriel, she will be ready for him when he inevitably eventually breaks out. It seems reasonable to assume that now that Madison knows the truth, she will work on building up her mental resources so he won't be able to take her over again. Of course, it's also highly likely that she'll be doing that from inside a prison cell, since even though we all know that mentally she was innocent of Gabriel's murders, the police aren't likely to let her physical body off the hook.
