The Joba Problem

Joba Chamberlain pitched 3 innings today, throwing only 35 pitches in the process. The reason the Yankees pulled Joba out of the game so quickly is because they decided that he will have an entire new set of rules. Joba will work his way up to being able to pitch a full game for the Bronx Bombers. The question is though....why? I know Joba has to have his rules, but why did they have to start all over? What happens if another pitcher gets hurt in the 3rd, has to leave the game, and they need the whole bullpen to be used then? Why now? I am disgusted at the way the Yankees have handled Joba.