While there is no way to use a source control system such as Team Foundation Server (TFS) or Subversion with PerformancePoint 2010, all is not lost. You can use the version control in SharePoint as your source control since all PerformancePoint items are now stored in SharePoint lists and document libraries.
If version control is enabled on the SharePoint lists and SharePoint document libraries that contain your dashboard items, you can easily view the version history for each item. And, in the event that an unwanted change is made to a dashboard item, you can restore a previous version of that item.
There is a good demonstration on how to set up version control in SharePoint in the article Configuring Version Control in SharePoint on MSSharePointTips.
While using the version control in SharePoint does not have anywhere near the functionality as Team Foundation Server or Subversion, it will still save your hide when you accidentally delete a dashboard that took you hours to build.
Note that this is not possible in PerformancePoint 2007 since it was not until PerformancePoint 2010 that you can save dashboard items in SharePoint lists.
Now we can only hope that one day Microsoft adds true source control to PerformancePoint.