Sera's openly spying on the hideout and almost gathered all the knowledge about it already. Since she's still an enemy who's trying to find a way to kill Youji, at this point, she's too dangerous to be kept alive. Since MC will just not kill her, 'cause he's a wuss, she should at least be restrained in the sense that she can't go back to the capital, or if possible be under the influence of Ria's memory manipulation magic.