Altium Storing to History Problem
Go to: 


  DXP -> Preferences -> Local History -> Number of days to keep documents in history -> [number]


Here you can set the local history. There is also an option for backup to a server, save auto saves in history and the auto save interval.  It's your auto save interval that is too short and the auto saves are saved in history.

The preferred model is save the last [number] saves but Altium16 does not have this feature. Depending on the project (importance), I would set the preferences. In your situation I would cleanup the history folder every day or two.

Automated backups will help a lot in recovery of old files. As long you are careful with changes it's not necessary to keep the history folder.