You can control who can see Appogee Leave in their Google App Launcher - sometimes known as the 9 box or "waffle" menu.
From the 9 box menu, click Admin > Apps > Marketplace Apps.
Appogee HR/Leave will appear here, to change who has access, click the three dots to the right hand side.
For instructions on how to turn on/off Appogee Leave for specific Google Apps organisational units please see this Google Apps Administrator help article: https://support.google.com/a/answer/172931