The only way to deactivate Messenger is to first deactivate your Facebook account. If you don't want to go that far, you can disable your active status, or just delete the app. Once you've deactivated your account, you can reactivate it by logging back into Messenger or Facebook.
Can I deactivate Messenger only?
However, if your Messenger account is connected to your Facebook account, you will have to deactivate your Facebook account first. ... Open Messenger. From Chats, click on your profile in the top left corner. Tap Account settings.
What happens if I deactivate my Messenger account?
Since you've now deactivated Facebook Messenger, that means that your friends and contacts will no longer be able to see your account or profile within the Messenger app. Nobody will be able to send you messages either.