Disabling the user registration from your website and only enable it through your app will not be possible as this feature is fully dependent on the BuddyBoss Platform. 

If the requirement is on top priority for your website, you will have to connect with your personal developer to make the required changes. You can share this great idea on our new roadmap. Head over to https://www.buddyboss.com/roadmap and click the + Submit idea button to suggest a new feature.