I'm still trying to figure out how the mouse community is viewed as the 'good' race of rodents when they send LITTLE BOYS down dark holes to be eaten by rats if they...well, are different. What the heck is this doing in a kid's movie?
I don't think they are. They're viewed as a flawed society that's only hurting itself by refusing to accept anything new or different. Isn't that a major theme in both the movie and the book?
Basically the difference is that the mice are a highly oppressive, stale society that refuses to accept anyone different, while the rats are an evil, cynical society. From a certain point of view, the rats could even be considered "less evil" because they, at least, are honest.
Actually, when you stop to think about it, they're Not So Different in that regard... both are headed by oppressive authority figures (the council and Botticelli, respectively), who keep the populace in check by playing to basic, primal emotions (the council being fearmongers and Botticelli running things almost entirely with Bread and Circuses), as well as callous rejection of anything different... the council throws people like Despereaux to the dungeons, while Botticelli is something of a FantasticMisanthrope, arguing that all rats are really monstrous deep down and rejecting the idea of them being different instead of the individuals themselves.
To put it in D&D terms, the rats are chaotic evil and the mice are more or less Lawful Evil, even if its only for self preservation.