Alma begins to give them the answer. He starts by indicating that they have desired to know what to do. As he begins this part of the discourse, however, something tells him that some in the congregation might misunderstand. Alma takes care to indicate that he is not judging them all to be humble only because of their humility. To parse the meaning out of his aside we examine it and perhaps restate it.
[now I do not desire that ye should suppose…] Alma is indicating that he does not want them to think that which follows.
[ that I mean to judge you only according to that which is true] Alma has pronounced a judgment on them. He has judged them as “compelled to be humble” in verses 12-14. Here he indicates that he does not solely judge them on that basis. When he says “according to that which is true” he is referring to the fact that they have been cast out of the synagogues. That is the true fact. It is on the basis of that true fact that he made the judgment that they were compelled to be humble. Now he indicates that he understands that this might not be the case for every individual in this group.