Could the guy at bat who gets hit charge the pitcher and wack him with the bat? If the pitcher can use the ball to try and kill you why would the league punish you for trying to use the bat to hit the pitcher?
Not using a bat as a weapon seems to be some unwritten rule of baseball. And rightfully so IMO, a bat could end someone's career, and falls squarely into 'criminal assault' territory.
Consider it a MAD strategy if you will - if YOU use a bat, then that opens the doors to someone using it against you(r team) someday.