You have to come up with a way to diable the auto follow during those abilities.

The easiest way is to set up an action target group for your toons. You then set up the auto follow to only send "follow" to members of the action target group. Now when you begin say a 3 second channelled ability, u have ur toon leave the action target group and rejoin in 3 seconds. This way the follow command will never be issued to that toon and he will complete the channel.

You can also do this for your DPS abilities so that you can continue to press ur DPS spam button but none of the commands are issued to the toon currently channelling.