The attached patch will add support for exclusion channels to the Flood module.
After patching, just add the following to your defender.conf:
excluded_channels=#chan1,#anotherExcludedchan,#etc
The configured channels will then not be locked when a flood is detected in them. Instead, the following message will be shown:
*** Global -- from Watcher.your.host: ALERT! #chan1 has been joined/parted 8 times in the last 10 seconds and IS NOT locked due to being an exclusion channel.
Diff of flood.pm from IRC Defender 1.5.2