You can't disable it but you can hide it to some extent. For example in the notifications back to customers you can remove any links to the issues so that they can't simply click on it and end up on the portal. You can hide all request types from the portal such that if a customer wants to go to the portal they would see the project but no request types to click on and open a request.
You may wish to vote and watch this issue JSDCLOUD-1547 - Ability to Hide Service Desk from Help Center
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