k:lines on a bot that can repeatedly attack is useless, use z:line instead (on the IP) as this stops the bot even knowing your server exists. A k:line allows a client to connect before being dealt with whereas a z:line is a firewall and disallows the connection initially. I think z:line is also called a d:line on some servers. Better still, if your IRCd offers a seperate command to store z/d:lines permanently then use that and there's a good chance that particular botnet won't be able to reoffend. Once again the list of bans may be big but this is better than being nailed.

People who run botnets to flood with have what is called small penis syndrome, amazing what turns them on ay. One last thing, there is nothing that can be done to stop the attacks but at least with the IP bans you can save your server from reacting to what is thrown at it.