I would suggest that any legislation will trump the covenant in this event. The parish council are responsible for the hall and ensuring its Covid-secure compliance and therefore if they are stopping everyone from using the hall, they are not singling out the Church. If there was an incident of Covid in the hall, they would be liable. Clearly they have considered the safest option is to complete close the venue.
Surely the Church could meet in its own building anyway? What would the church want to use the hall for? If its for drinking tea or coffee after the service, that is banned by the legislation....