The Bana are immortal, but it was actually Circe who did it, not the Patrons; it was part of their devil's bargain with her, which WML explains *really* poorly, but which does nevertheless seem like something she would do. There's never really been any discussion or even mention of what that means, exactly - you'd imagine it would be a source of tension between the two cultures, and unease within the Bana culture (what happens if Circe revokes this, and where's the catch), but if so, it's all happening where we can't see it.
As for the guys in the breeding pens, and the slaves in the furnaces, Diana didn't free them that we ever saw, which is yet another reason that the "oh, the city's gone? meh" response at the end rings disturbingly.