AD sync messed up SEP Clients Group Membership

I have SEPM 12.1.6 installed on Windows Server 2008 R2. I created three SEP groups named HR, Finanace, IT and move all the clients in their respective groups.

We have a requirement for different users logging in to SEPM console with AD credentials. So i did Directory Integration. After AD Sync all the computers that were in SEP groups automatically moved to AD Groups. This was an undesired outcome. How can i avoid this while still retaining the ability for users to log into SEPM console with AD credentials?