I think we've got logic on our side in what we're saying, but this is a case where tradition carries a lot more weight than logic. I'm not looking for MLB to rush to re-examine this.
But ... just for the heck of it, I looked up some stats for a few players and compared their lifetime BA vs what their lifetime BA would have been if sac flies were counted as an AB.
Here's what I found:
Albert Pujols:----.333 actual vs .329
Dustin Pedroia:--.302 actual vs .299
David Ortiz:------.282 actual vs .279
Derek Jeter:------.317 actual vs .315
Eddie Murray:----.287 actual vs .284
And for what its worth, Eddie Murray is the all-time leader is sac flies (with 128).
So while changing the rule to count a SF as an AB would cause batting averages to drop, it's not by as much as I would have thought.