Before one attempts to answer questions of this kind one must be sure that one is aware of the precise circumstances of the case. From what you say, the Parish Council is the sole trustee of the charity and not some or all individual members of the council. That being the case, any decision of the trustee (the council acting in its own legal capacity) must be made according to agreed processes. Unless the council chair has the express authority delegated to him (under the Standing Orders for example), the decision you refer to can only be made according to the normal processes of the council, ie by discussing and determining a motion at council.
I am assuming that the management committee does not appoint the manager.
The plain fact that the clerk is also the manager would not in itself be an issue.
I hope this helps