RailCraft and Actually Additions have breeders that work nicely. The system you described with baby filters should work nicely. A servermate set up something similar with three rooms. Top floor is the breeding room. Babies fall through the floor into the baby room on floor two. When they mature, they fall through the floor again into the kill box with an upgraded Mob Masher.
I did have to personally install overflow protection to prevent it eating our server once his inventory was filled. Easy enough to do with a Storage Drawer with Void Upgrade and Redstone Upgrade. Once the drawer is full, it shuts down the breeder, then voids the drops of any overflow still maturing in the pens. If you want to keep all the drops from a multiple drop animal (cow; steak, leather), you can have a drawer for each drop linked through an And gate. The Void Upgrade should take care of the excess while the lesser tops off, and when everything if full, the redstone signal shuts down the breeder.