Mike-
 
When I first started keeping bees - about eight years ago -
I had the same remorse over squashing bees as I closed up
the hive.  I still do squash a few, but I have developed
a system that works for me.  I let a little smoke float across
the top of the hive body (to give me a head start).  Then I slowly
lower the inner cover down about twenty degrees of of its final
position.  this rotation gives me a smaller surface area for
squishing the ladies.  If I lower it slowly enough, they all get
out of the way.  Once the top is down, I rotate it slowly, hoping
to chase my small cohorts out of the way.  This seems to work for
me.
 
Larry Krengel
Marengo, IL USA