Eeeeek, well that would work, but it's only a solution if the bot is just in one or just a few channels.
Each time you add a chanel to the conf you need to restart the bot to get the changes working.
The solution Mr. Snake told, just to add the channel dynamic by using .+chan #channelname ist IMHO the better and more comfortable solution.
And for what use will be this pub !join when his eggdrop is not in any channel at all? Anyway, telnet or dcc in then see the .help +chan as you where sugested before me.
Adding a channel directly in the .conf file will make it static, so your eggdrop will be unable to "forget and erase" it from it's "memory" (channels file) when a dynamic one can be erased at any time. Also the static and the dynamic channels can be "parted" using the +inactive channel flag.
Once the game is over, the king and the pawn go back in the same box.