The imagery of the fruit is here based on the same concept as Matthew rather than the fruit of Lehi's tree. This imagery does not depend upon eating (or accepting) the fruit (the gospel) but rather upon one's actions after the fruit has been eaten. Metaphorically, Alma is using a concept that we might know as "you are what you eat." In this case, Alma expects that the effect of the gospel upon the person is to create a transformation - a "mighty change" (verse 12). The change in the person will change the nature of the "fruit" he produces. The fruit is the metaphor for our actions, and the change in us will change the nature of our "fruit" or actions. Alma suggests that if the actions have not changed, then the "mighty change" has not occurred, and we will be under condemnation.
For Alma, it is not membership in a church that provides the benefits of the gospel, but the changes that the gospel effects in us that are the important aspects of the church. Alma is preaching to people who claim to be members of the church, but who are guilty of "all manner of wickedness." The membership in the church does not automatically erase these sins, and without a renewed repentance, those people will surely be condemned before the judgment bar of God.