You can remove a site from a SharePoint Online app.
Procedure
From the navigation pane, go to Protect > Office 365.
The Office 365 apps page appears.
In the Name column, click the app that contains the site that you want to remove.
The app page appears.
Perform one of the following tasks depending on the entity you want to remove:
On the Sites tab, in the row for the site that you want to remove, click the action button
, and then click Manage > Remove from content.
On the Content tab, in the row for the group that you want to remove, click the action button
, and then click Manage > Remove from content.
A confirmation dialog box appears.
Click Yes.