Bizarre question, but is there any way to completely disable the functionality and ability for a user to configure Scrivener to sync with Simplenote and Index Cards for IOS?
No, there is not a way to do that, though it should be noted that if you never use them or set these up, they will never be used. Only folder sync will actively attempt to update the project or the sync folder on project close/open (a behaviour that can be disabled). Simplenote will never do this because of how long it takes to poll notes with the server. Index Card, when you look at how it works, is actually more like import/export than what we would traditionally think of as synchronisation.