In options/irc/flood I assume you've checked "enable flood protection". Does the bot also have checkboxed "own messages" too?
barring this, the relay could use a @que window and a timer to control the flow of messages. Instead of relaying the ON TEXT from #channelA to #channelB, it could output the ON TEXT from #channelA to #channelB as "/echo @que $network %DestinationChannel %message_text", and then a timer would check @que for a line whose first word matches the $network at which that timer is running. However, the script would still need to know what's an acceptable rate of outputting messages per network.
