As of now there is no way to remove user-added applications as an Okta Admin. The only control you do have is what applications your users can add. The scope of what those applications are can be modified within the Applications -> Self Service -> Settings tab.
The same goes for what we call on-the-fly applications. Those on-the-fly apps are also listed in the User Added Applications box. Currently we can only turn this on-the-fly feature flag on/off for your entire organization.
This could most certainly be a feature request! Please let me know if you have any other questions.