Here's something else to consider with instant replay: How do you deal with an overturned call?
Example: Original call is a foul ball... There is no way to fix this... The play dies as soon as the ball is called foul... Runners stop advancing... You would simply be guessing at where they would have ended up if the correct ruling was made... You also remove the possibility of the defense making a play on the batter-runner or other runners... There is no good way to make the call "right"...
Example 2: Runners 1st and 2nd, 1 out... Batter hits a sinking line drive to right field... You have a trap situation on the catch by the right fielder... Original call is no catch, so runners advance... Runner from 2nd scores, and runner on 1st ends up on 3rd with the Batter-runner on 1st... Replays show that there infact was a legit catch by the right fielder...
Where do you place the runners in the overturned situation? The runner on 2nd could have tried to tag up and advance to 3rd... The Defense has a good chance at getting a 2nd out if the runner goes... You can't just give him 3rd for free, but at the same time, you can't deny him the chance to legally advance... Again, no good way to make the play right...
This is a very slippery slope when talking about replay in baseball in regards to live ball plays... Most plays have several cause/effect scenarios based on different rulings, which in turn, give you a vastly different result... It's near impossible to give a ruling that doesn't screw over the offense or defense...