This is interesting stuff, Now Microsoft Azure Virtual machines (windows and Linux) can be managed through on premises ConfigMgr SCCM 2012 SP1 and above. The Endpoint protection 2012 SP1 can be used for Azure Vms. Microsoft has released a KB article on the support scenarios. Read more from here (kb/2889321).
Two supported scenarios here….
1. Use an existing on-premises Configuration Manager infrastructure to manage Windows Azure Virtual Machines that are running Windows Server or Linux through a secure site-to-Site connection.
2. Set up a single stand-alone Primary site in the Windows Azure Virtual Machines environment to manage Windows Azure Virtual Machines that are running Windows Server or Linux in the same virtual network.