*adjusts unneeded glasses*

Well, yes, unfortunately, the cartoon is canon. It's published and authorized. As much as I hate to say it, the cartoon is part of the world. In a way, it is a world unto itself- as you say, there's a large size disparity. In the books, there was also a difference, but it wasn't quite so large. I'd say mice and rats would have had no more than a foot or so of height difference, or equivalent. Badgers probably would have been eight or nine feet tall or equivalent. Maybe ten for larger ones like Gorath. Hares might have reached six and a half as opposed to a mouse's five and a half, and I'd put foxes as five-foot-nine.

It all depends on whether you're writing for the cartoon or the books whether the sizing is correct. A mouse from the cartoon would probably be actual mouse-sized in HQ, like a mouse from Narnia, Celestia damn the place, while a mouse from the books would be able to look you or me in the eye and then claw it out if ze so desired. Good luck!

I'd suggest looking up the Redwall missions and agents on the Wiki. IIRC, the agents are all roughly around the same size as a human, and the buildings and trees in the canon seemed to be the same size to the animals that real world buildings and trees are to us.

Also, I never noticed any notable size differences in Redwall agents.