If what occurred is as described, the chair should have verbally reminded the clerk that they should not interrupt a council meeting and ask that they moderate their behaviour in accordance with Model Standing Orders para 2 (or what ever that council has adopted) and then follow the guidance of sub paras a, b & c if necessary.
As a follow up, and in relation to the described incident, there should be an immediate initiation of a disciplinary process with suspension pending outcome a strong possibility. It the outcome is any less than gross misconduct it is likely that the process has been bungled.
Since it is reported that there is a "history" of such behaviour from the clerk that might indicate that there has been, or remains, a reluctance or inability to adequately address the matter before it became publicly problematic.
Is the chair a liar?
The clerk doesn't have any form of 'privilege' or 'protection' so they may be creating a defamation unless they have a reasonable defence...