Agree with the above that tames can get very friskey an do incidental damage in their desire to get at enemies outside the base.

One thing that has definitely helped us was placing wards. My wife and I play co op a lot and occasionally with other buddies so we came late to using the ward, but I have found that its wide radius does seem to make sure there is no spawn gap in between workbench coverage.
Maybe give that a try?

But yeah as of now the only fix is raising or lowering the ground to stop things running amok. I really hop ewe get a more balanced solution as its getting cheesy: troll attacks dig a ditch, Fulings? Ditch (or earthworks) animals skittish - Ditch, Golem in the montains near you - ditch/earthworks etc etc etc nothing else works long enough to be worth the effort!