Regardless of the intended message (if there is one), I think that we should think of Rodrigues as either not loving Christ or as having a defective love for Christ. He says that he still loves Christ but that his love changes, and perhaps we should take him at his word, in which case we opt for a defective love rather than none at all. His love is defective because he has valued this temporal life and lack of temporal suffering (good things no doubt)--for himself and others--to the eternal, and he thinks that his love is the love of Christ. But Christ never renounces God for others. Christ's shame with which Rodrigues comes to identify after apostatizing, is the shame heaped upon him by others and not the shame as the result of denying God. Rodrigues also seems in the end to adopt the Japanese cultures' fatalism which influences his understanding of Judas' relationship to Christ as well as his own. He comes to see Christ as commanding Judas to betray him, or at least to get over and done with what is inevitable. This probably helps Rodrigues to mitigate his own sense of shame for his ultimate failure much like the ancient Stoics invocation of the Fates. His only shame, in the end, is the shame heaped upon him by his fellow priests and other Japanese. Rodrigues never confronts his tormentors when they are invoking their fatalist dogmas to insist that they are in fact free not to torture the farmers. Instead he comes to believe that it is he, and he alone, who is responsible for their suffering. It is he who hold the power.
The book still leaves unanswered the question of what is wrong with trampling on an image of Christ and saying that one denies Christ even if one loves Christ, believes he is the savior, knows that others will suffer if one does not, and so on. It's not hard to imagine, for instance, that a father would tell his children to trample on an image of him and say that they do not love him if it would save them from being tortured by a terrorist! It's not hard to see how a father could do this out of love.
But then we are not God. And what about the children's love for their father? Could it be that perfect love is inconsistent with expressing what one believes is false about one's love for another? And could it be that perfect love is always required of God even if not always required of us to each other?