Gohan said
Because. Gilgamesh's all-healing water heals everything, no exceptions. It's already been done, Weiss's affliction's are gone or whoever it was from Team RWBY. You can't just not go through with something that's happened, because it doesn't "work for you". YOU LOST IT'S NOT SUPPOSED TO BE IN YOUR FAVOR. If I were you I would do research on someone before engaging in battle with them. They are no longer mad. If you can't play as thrm, you have to just not play as them and move to your other characters.
Mia's insanity was completely washed away, She is a fully functioning human without any inherent insanity in her. Of course, the problem is that memories are not an 'affliction' and any normal functioning human being with a conscience would be sent into a catatonic state from the sheer guilt after the untold acts of horror she had committed. This is not her previous insanity, it is her reaction to this new situation.
Stein's keeping of his insanity I can see could be more doubted. His background is that he was always a bit of a sadist obsessed with dissections. However, he was able to control his urges and get along with others. Despite his personality, he attempted to be a good person. And succeeded. Then, he faced the Kishin, a 'demon god' of insanity, the original user of the Madness Wavelength. This strengthened Stein's madness, and after Stein killed the beast, earning him the title God-Killer, he devoured the Kishin's soul, and merged with it. This was the last act the Kishin's insanity forced him into. Even in victory, he doomed himself.
To heal something is to return it to it's natural state. If you heal a dragon, it will not become a human, even if scales would be 'healed' away from a human being, because they're not supposed to be here. As such, healing the Kishin would do nothing besides restoring it to it's full personality. As such, in order to retain the awesomeness of Stein, I've ruled that Stein is cured, and the Kishin within him is not. Or rather, is, but still insane, as that is the Kishin's natural state. If you believe that this makes no sense, then please state why you believe that, and like I said, if I believe you to be correct I shall edit.