I agree with Mentorman that there is an important role for the clerk here, but ultimately this is an issue of personalities. Too many clerks lack the knowledge of the law and rules of engagement, so are not in a position to intervene effectively.
Training is the key, but I'm concerned that some ALC training appears to brainwash clerks into believing that they are in charge, making them unduly belligerent in their communications with councillors. I have seen several cases where this breakdown in the relationship resulted in the clerk being forced out of their job.