Sometimes, a story is weak in some places in order to be strong in others. Redwall (And fantasy in general) tend to take certain races, and make them naturally evil, in order to better examine the actual conflict between good and evil. If Orcs (Or Rats) were complex beings who differed from the humans (Mice) only in upbringing and environment, raising moral quandrys about killing them indiscriminately...well, it might be a good story. But it wouldn't be the story that the author wanted to tell. So they make an organism naturally infused with evil, and make them inhuman in order to discourage people from looking at it from a racist perspective. Then you can focus on a good versus evil epic filled with streamlined heroism, self-sacrifice, and gritty determination. This is fine: Imagine if Die Hard was filled with a in depth understanding of the main characters childhood fears, or if a good chunk of The Matrix was scenes of Neo and Trinity dating, and Neo getting over his intimacy issues. Those things are not important to the story as the creator wants it told, so they are glossed over. What the story loses in realism it makes up for in being streamlined and focused.
The one thing that strikes me as potentially slightly racist in Tolkien in particular is within human lineages. Certain bloodlines are strong, and make good leaders, while others are weak and watered down. Having some humans inferior to others may be plot necessary, but its a little awkward.
