How can an email be sent anonymously? The email address would be included in the message? It is unclear fro your post if the Clerk received the email and has anonymised it under instruction from the parishioner or if the parishioner used an unidentifiable email address and left the email unsigned?
Some councils will have a policy that prevents anonymous correspondence being raised at meetings as there is no method of reply.
That said, I don't believe it is against GDPR as the parishioner sent an email in for a specific reason and clearly anticipates is generating action from the parish council. I believe councillors have the right to know who is the correspondence is from.