Originally posted by Kvarig:

So basically build a giant box fully enclosed is the only way to protect them...wow thats great... I'd much rather be able to have a more realistic looking farm and not have to build some crazy industrial breeding camp with a giant pit roofed in stone with only a portal for entry.

You don't need a giant box, I've built a realistic looking farm with a barn and barnyard. The barnyard has pigs and chickens wandering around breeding, inside there are stalls on each side that enclose pairs of wolves and pigs incase the ones outside get wiped out. It's also a good idea to keep a pair secured in a second location for boars just in case.
Also spawn protection helps out alot so you don't have to worry about ground raids, learned that after I had a swamp raid and an oozer poisoned all my pigs through the barn walls but thankfully a piglet survived. Bats don't hurt anything as long as they can't get through the windows.