The issue is not that it was inconvenient for several hundred people, the main issue is the warrant covered. Allowing the FBI to search not just the remailer, but giving the FBI full access to poke through and grab whatever information they wanted from the entire server.I would not want my apartment to get searched because someone else in the building did something.
And sure, you can justify it to yourself that it was to help other people, but the point is there is a precedence out there now [or was it there already? i haven't researched that]... if someone uses gmail and sends a bomb threat, confiscate all gmail servers, and have access to everyone's accounts. That sounds legal, that sounds right. That is NOT an invasion of privacy.
Even if you agree with the cause, you cannot give carte blanche to the FBI to do whatever they want with the entire server. Make the warrant be specific. They can only search the information about the remailer. If they want anything else on the server, that is a different warrant.