We have no indication that Alma the Elder knew the extent of his son’s participation in the persecution. If he knew that, it was not recorded. In fact, it says in Mosiah 27:10, "He [Alma the Younger] did go about secretly with the sons of Mosiah seeking to destroy the church." The main point is that the king and Alma the Elder were worried, and they were trying to do everything they possibly could to help the situation, but neither of them knew what their sons were up to. It was, therefore, up to the Lord to see that the situation was changed.