As shown at the beginning of the movie, using the EMP doesn't damage anything in the ship, so why did they have to wait until Neo was out of the Matrix to use it ? Even if it only damages online systems, they don't cut the power like they do the first time they use it, so that wouldn't justify it. Am I misunderstanding how their EMP works ?
If they had used it, they would have killed Neo because he'd still be in the Matrix. They used it the minute he was out, and absolutely destroyed the electrical systems of the ship. An EMP would only not damage the ship if the circuits inside the ship were disconnected, that is, turned off. That's why we see them do that when they use it the first time. It probably stretches the reality of how EMPs work - but this is the fiction the movie works in.