You could either cart them or use water channels, which ever you prefer, and move them a minimum of 32 blocks away from your breeder, as to not effect your breeding rates. Once that distance is met I usually just drop them 40-50 blocks down a 1x1 chute with lava at the bottom, just in case ;-). 100% death guarantee... Using water channels, this is relatively easier. With a minecart system, you'd have to develop a device that drops the villager while retaining the cart, unless iron isn't an issue for you, but then again it's still wasteful. If you're more of a technical player then this may be more appealing, but I usually just go for water because it's more convenient.
Was just about to post something about water channels then saw your post, haha.