Wow, I can't believe I forgot to enable autoconnect, I use that quite often on my own board as well. I will release the fix (and instructions how to enable autoconnect for your channel(s)) soon, if there are no more bug reports. The next scheduled bugscrub is Friday, but it can easily be changed if there are (as mentioned) no more bug reports.
As far as Mibbit goes, it's not really a middle-man type of thing, it's more of them hosting a client so it doesn't use any bandwidth on your server. Mibbit does not interfere with the way your channel runs, and does not effect your channels.