That's a tough one. Depending on how you automate, you could use a combination of other programs. For instance, if you have some sort of CI system, you could automatically compare the files in source control to a live database using SQL Compare and tell it to synchronize. You would need the source control system's command-line interface to check the changes back in.
SQL Source Control, as a piece of software, was designed to work interactively only.
If you want to do this in code (c#, VB), then you could leverage the source control system's API to check in files if they have one. For instance, SVN has "SharpSVN" and there is also an API for TFS.