Answer
If you only want to keep the Messenger service, you will need to deactivate your Facebook account for a second time. And keep in mind that if you delete your Facebook account completely, you will lose access to Messenger as well. Sadly, there is no way to keep Messenger without maintaining a Facebook profile.
How to Deactivate Your Facebook Account but Keep Facebook Messenger
How to Uninstall and Delete Facebook Messenger
Can you delete Messenger and keep Facebook?
If you only want to keep the Messenger service, you will need to deactivate your Facebook account for a second time. And keep in mind that if you delete your Facebook account completely, you will lose access to Messenger as well. Sadly, there is no way to keep Messenger without maintaining a Facebook profile.