In order to be able to unassign a channel, it needs to be closed first. Note that most of the parameters of an ANT channel, like the channel period, can be changed on the fly, while a channel is open.
Have you looked at the background scanning channel functionality of the AP2? This might suit your needs better. There is more information on this feature on "AN11 ANT Channel Search and Background Scanning Channel", at the DevZone.