The "looking-glass" might be a lens for the way Indians (Native Americans) see white hypocrisy. But Apess is using the looking glass as its more direct definition of a mirror. Thus, the Indian holds up the mirror so that the White man can see his own hypocrisy.
Apess uses Bible passages and historical evidence to support his argument that it is illogical, unethical (against Jesus' teachings), and therefore hypocritical for Christian whites to view and treat Indians as second class citizens. Furthermore, he questions the purpose of missionary work if those who are converted are still treated as inferior. Historically, missionary work has often been in conjunction with colonization.
I would ask: What is all this ado about missionary societies, if it be not to Christianize those who are not Christians? And what is it for? To degrade them worse, to bring them into society where they must welter out their days in disgrace merely because their skin is of a different complexion.
The irony is that these missionaries and Agents (white officers who oversee Indian affairs in Massachusetts) who are self-proclaimed Christians have mistreated Indians and this goes against Jesus' teachings.
Apess notes that it is even more ironic/hypocritical considering the historical supposition that Jesus himself must have had a dark complexion.
Now, if the Lord Jesus Christ, who is counted by all to be a Jew - and it is well known that the Jews are a colored people, especially those living in the East, where Christ was born--and if he should appear among us, would he not be shut out of doors by many, very quickly? And by those too who profess religion?
This is perhaps the ultimate irony. If Jesus were indeed "colored" or "non-white" and then appeared in America during Apess' time, he (like other Native and African Americans of this and subsequent times) would also be treated as an inferior simply based on the color of his skin.