Consider placing two breeders on a balcony above your breeding pen - but still inside the radius of your feeding station. Surround the base of the breeding pen with Mystcraft crystals, and in the wall, a concealed mechanism to place and remove a linking book. When you hit the lever, all but your base pair of breeders will be teleported to your cooker area/killing floor/whatever. Hit the lever again to deactivate the portal, and let your feeding station repopulate the pen.
I was stymied in my attempt to set this up earlier - but Redpower will make the book placement and removal much easier. A sorting machine or manager will also make it simple to send a set amount of feed to your feeding station to create a set number of animals per push of a button.