It sounds to me like you're taking the book out of its cultural context and bringing it into the 21st century. When Lee wrote the novel, black men were being put in jails all through the South on testimony as baseless as the one given against Tom Robinson (and of course, black innocents are still disproportionately convicted and jailed, but that's another topic).

Saying To Kill a Mockingbird engages in its own form of racism seems like saying early feminist works engage in their own form of sexism, because instead of talking about the equality of sexes they merely talk about the positive qualities of women. I think the time period in which these things were written has to be taken into account.