If MKS offers a command-line, you may be able to configure it with config files – see http://www.red-gate.com/supportcenter/Content?p=SQL%20Source%20Control&c=SQL_Source_Control/help/2.2/SSC_working_with_config_files.htm&toc=SQL_Source_Control/help/2.2/toc1432725.htm
MKS is a source control software that is very powerful and allows issue tracking and source control to be linked. It doesn't cope very well with .sql files though, so being able to plug SQL Source Control in would be great.
You can find more info here: http://www.mks.com/.
What is MKS?