While I am not sure what all the rules are involving instant replay, I do feel that it is a valuable tool to make sure that the game is called fairly. If you have a tool that could used to mediate a dispute why not take advantage of it. Yes it may cause delays in play.. but if a play is questionable... use the replay to make sure that the right call is being made.
Any call that can be corrected through instant replay should be corrected through instant replay. We have the technology to get nearly every call correct and choosing not to use it is ridiculous. Instant replay will not increase game length because on close calls the umpires are already taking a long time to discuss the call. Instant replay would actually be quicker in many instances. Baseball is a multi-billion dollar industry and it owes the fans, and the games, a game that is consistently and fairly officiated.