Yeah, I started with fences but my cows and chickens kept escaping. So I dug a 1-block deep pit with fences on the top, same thing. So now it's a 2-block deep pit and they keep walking into walls and dying. Although the best source of livestock deaths so far was Thaumcraft. I pushed my flux way too high and the aura purged it via lightning strikes. For some reason, it loved hitting my cows. I went to my pen after several strikes to find no less than 3 separate piles of cooked steak. 
I decided I might want to cover my pen from that point on.
I decided I might want to cover my pen from that point on.