How about fighting fire with fire? Cast Insect Plague. 

I've read a lot of griping and groaning from DM's who've claimed that it can drop things below 1, meaning that it's an insta-kill for most regular animal types that you'd encounter, because even a rampaging dire bear will just flop over if it takes 2 damage. Might need to check into this one a little more...
Ray of Stupidity is indeed a problematic spell against animals and does need to be changed or banned. However, as a ray, it is useless against swarms (unless we're thinking of different spells). I am not aware of a spell that does Int damage in an area.Ok, so I found it in Spell Compendium. It deals 1d4 + 1 Int damage, so yes it can drop the target to 0 and so into coma. It has SR and no save, so the swarm in the OP would have around a 50% chance of dropping from one such ray.
It's probably not a spell I'd allow in play, but then I usually limit things to core only.
5 CR 10/11 v 6 Cr12 = TPK
The Swarm is a CR12, and has the typical SR for a critter of that CR. Also a direct damage caster has had plenty of time to pick up spell penetration and Greater Spell penetration. However, the Saves are pretty high and evasion was just cruel for a monster given a ton of HD to bloat it's HP.This swarm seems to be designed to reverse conventional wisdom for dealing with swarms: Area effect spells are more or less a no-go.
Ray of Stupidity is indeed a problematic spell against animals and does need to be changed or banned. However, as a ray, it is useless against swarms (unless we're thinking of different spells). I am not aware of a spell that does Int damage in an area.