The angel who appeared to Alma never directly told him to repent. Why is that? Well, the message about repentance is actually there in the first half of this verse; it’s just not explicitly spelled out. Alma was told to "remember the captivity" that is a consequence of disobedience. That phrase will to lead us to repentance, and we can even see that same language used by Alma in several of his own sermons in the book of Alma.
The angel of the Lord said, "Alma, go thy way, and seek to destroy the church no more, that their prayers may be answered, and this even if thou wilt of thyself be cast off." It is not immediately clear what "cast off" meant. It may have meant that Alma would have been banished, excommunicated, or disciplined under the church rules established under Mosiah 26. Later, when recounting this experience, Alma warned his sons that if they didn’t "keep the commandments of God ye shall be cut off from his presence" (Alma 36:30, 38:1). All of this indicates the ultimate spiritual significance of what the angel was telling Alma.
In Alma 36:9 he records the angel as having said, "If thou wilt of thyself be destroyed, seek no more to destroy the church of God." This language is even more powerful. It is possible that Alma was in some sort of physical danger, much like Sherem was in the days of Jacob. He was certainly in spiritual danger. When recounting the angel’s warning later in his life, Alma immediately explained that he "was racked with eternal torment, for my soul was harrowed up to the greatest degree and racked with all my sins" (Alma 36:12) and was "tormented with the pains of hell" (36:13). Alma actually would have preferred to "become extinct both soul and body" rather than "stand in the presence of my God, to be judged of my deeds" (36:15). Again, this suggests that the more weighty destruction that Alma faced and feared was spiritual in nature.