Usually your big strong guy is a better bet for a sac fly than a sac bunt. Maybe that's what they were thinking. The problem you face is, if you pinch hit for him you may as well tell him to bunt out loud because giving signs is pointless. And if you let him stay in and swing, you could see an unproductive out or worse, a DP. A true Hobson's choice, so it's tough to criticize the coach's decision either way.
Personally, I would probably let him swing away and hope that either he or the next guy would come through with a hit. I might start the runner at some point, though, to try to avoid the DP and maybe get the ball thrown around to score the run that way. This also enhances the possibility of maybe even starting a multi-run rally so as to win, not just tie. It could put 2 guys in scoring position, force an intentional walk and get you a bases loaded situation for added pressure on the pitcher and the defense.