The reason for the rule is historical. From the dawn of time (or even before that, back when Billy started officiating) a held ball resulted in a jump between the two players involved.
Back in the day, the height disparity was more significant because you might have a jump ball at any point in game, and it might occur near either basket. Now that the jump has been relegated to just a way to start the game, it's no big deal. If the 5'4" kids loses the tap, his team still has 32 minutes to make up whatever points were scored off of the play.
It's only happened to me a couple of times, but it's kind of fun to see the look in the 5'4" kid's eyes when you tell him he's jumping.
BTW, the dust cover of my copy of "Calling The Shots" shows Earl Strom signaling what looks like a jump ball between two specific players. That's the same mechanic I have used when this has happened in my games.