One trip through an area ( hunting bushy tails or not) will not keep any game from coming back to that area later. It is REPEATED visits to the area that will make them avoid an area. If you shoot a few squirrels today, the deer may avoid the area for a day or two, but once they figure out you are not there all the time, they will resume their activities as normal.
It's kind of like finding doggy poop on your carpet. You will avoid it till its gone, but once it is removed and cleaned up, you will walk over the area as normal. ( Don't know how, or why, that went through my mind, but it seemed to fit.):
I know lots of guys who shoot squirrels out from under their feeders, and it doesn't seem to bother the deer coming back to them.