Maurice and Dangerous Beans die, and Death shows up to claim them. This leads to a touching and amusing scene, admittedly, but there's still something odd about the situation. Beans is a rat. Unless there's a forgotten explanation, shouldn't the task of claiming him have gone to someone else? Squeak.
At the end, the people who continue to put down traps and poison after seeing the Clan are described as having minds that "can't be changed with a hatchet". Seriously? After all of the protagonists have no problem with killing non-sapient rats, including the Clan themselves, this is the Aesop you go for?
It's by no means true that none of the protagonists have a problem with killing non-sapient rats. The older rats don't, and the younger ones let Maurice away with it because, well, he's a cat (and you can always trust a cat to be a cat), but:
It's not the fact they're still using traps and poisons that Terry's criticizing there, it's the fact that they do so thoughtlessly, just because it's what they've always done. People whose minds were more open would at least pause to wonder if there's an alternative, or if they might be unwittingly killing other sentient rats like the Clan.
The implication that they're the same sort of people who would cheer like mad for a sports team or musical group whose members are of an ethnic minority, then thoughtlessly go right back to treating people of that same ethnicity with prejudice, is there too, if you're looking for an Aesop in all this.
Right. It's not just the killing, it's the fact that they "ooh" and "ahh" at the amazing rats and buy rat mugs and eat rat burgers (with no rat, of course) and cheer at the rat clock, and then they cheerfully go home lay down the poison and traps just as they always do. You'd think they'd at least pause to think that maybe what they're doing is cruel, and that they'd decide to use non-lethal traps instead to let them loose. There is a drop of dissonance in that there's clearly a difference between the sapient and non-sapient rats, but the point is that the humans aren't changed by their encounter with the Clan at all (apart from the humans of Bad Blintz, of course).
Although our rats were a bit confused by the idea behind non-lethal traps and suggested it was useless.