Please follow this to disable auto-login after payment via WooCommerce.
#1. you need to set “Disable auto login” to Yes
#2. Create a page and use the following shortcode under the page content, this shrotcode will display a message and kick out the user from logged-in.
[user_verification_message message="Please check email to verify account first"]
#. Set this newly created page under “Redirect after payment” option