I think we take the peeper shot because we, or, more properly, society, places less value on a squirrel than a deer. It's part size, part eyes, part perceived intelligence, and mostly, conditioning. A wounded ground squirrel dragging itself through a backyard garners less attention than a deer. It helps if we can put a critter in the "pest" category too.

100 years ago there were fewer deer where I live. Either way,taking the long shot for food would have been societally acceptable.