Whether it’s right or wrong, when people who know what IRC is hear that IRC is involved in something, they immediately think malice.. This is not without foundation as a lot of antisocial behavior takes places on IRC channels. The other thought is botnets which use IRC to bootstrap, control or communicate. A program which connects to IRC is by definition called a ‘bot’ and to IRC people that means something bad, especially if it’s not an IRC bot program specifically.
What Satoshi did here is use IRC simply as a matchmaking service but I could see how someone could draw the wrong conclusion when they see a channel with hundreds of randomly named bots idling in it. Perhaps you could put these people’s minds at ease if there was some pop up asking them if it’s ok to bootstrap from IRC.. because if they just write it off as a trojan or botnet they may never bother to find out how it really works.