In verse 41 Alma suggests that “all things” are a testimony to him of the existence of God, yet Korihor denies God, even with access to all of the same evidence. What Alma does in verse 42 is level a terrible accusation. Just as Alma accused Korihor of declaiming a priestcraft that he knew did not exist, so too does Alma accuse Korihor of denying God even though he does believe.
Alma must have had confirmation from the Spirit that Korihor was in such a state, a state that would have been allowed if he had been an apostate Nephite as has been suggested. However, we should look more closely at verse 42 to understand what happened to Korihor. The key is that Korihor has “put off the Spirit of God that it may have no place.” Korihor began with faith, most likely a faith of his youth, and probably of his parents. What he has done is actively deny that understanding of his youth – he has been converted to the more secular Lamanite philosophy. He has been able to do this because he has changed his definition of where he might find evidence, or proof (as will be evident in his next statement).
Alma’s strong evidence for his understanding of God and Christ are all based on the Spirit, and Alma knows that this is the only true source of such knowledge. To deny God, Korihor has had to deny the Spirit, and thus deny his only possible source of that knowledge. Alma is suggesting that God is not reachable through a scientific or logical approach, but only through the Spirit. Korihor’s denial of the Spirit has led to a shift in what acceptable evidence was, and led Korihor away from the very things that would have given him a knowledge of God.
What is worse is that Korihor’s denial of the Spirit and God in his own life has led to a crusade to attempt to deny it in others. This is not atypical of the experience of one who leaves the church. The process of denying their own previous understandings leads many not only to deny, but to actively attempt to bring others to their new understanding. As Joseph Smith found out early, some of the most difficult pressure against the church came from those who had once embraced it, then left. Once again, this need of Korihor’s to have others follow his path suggests that he had been a Nephite believer at some point. All indications point to that change in Korihor’s life.