Mosiah declines to judge, and returns the problem to Alma. We are not told why Mosiah declines.
The logic of the situation tells us that Mosiah saw this as a religious problem and therefore one to be handled by the religious authority. It would appear that one of the problems that Mosiah was dealing with was a diverse social group. The introduction of the churches allows Mosiah to rule over a kingdom of diversified beliefs without necessarily dividing the community. It is perhaps in this light that Mosiah declines to judge.
We know that Mosiah is a believer. We may assume that he would be in sympathy with Alma's teachings since he installed Alma as the religious authority. It would also appear that Mosiah has taken the stance of separating the religious function from its direct ties to government.
The only good explanation for this move is an attempt to govern in spite of real religious differences in the community. By giving the decision to Alma, Mosiah can separate himself from that decision, and therefore from the possible social repercussions that might come from it. Mosiah is retaining his ability to govern the entire body, which includes an increasing number of people sympathetic to these religious dissenters.