The cloning issue is not relevant here because when a botnet nails a server they most often are one client per host, same as most chatters.
Read
here where I describe how the botnets most often work.
About channel holders in place of bots. That's possible if that feature is coded into Services however ChanServ, to my knowledge, won't ever kick for things that mIRC bots and eggdrops can, such as foul language or flooding. Perhaps this could be coded into ChanServ (I'm not suggesting it should, I just speak of the physical possibilities) too but that would ruin things for those that like to make their own custom-built bots and run them. Bots are, at times, a hobby in themselves and any network suddenly refusing to allow the friendly bots would probably be the next target for the hostile ones. Even networks that specifically forbid bots usually turn a blind eye if the bot in question does not cause grief.