I see you've had one reply over on SSC- I couldn't tell from your original post if you do have just a subset of the database currently source controlled right now though?
One other option we came up with is to look at filters- you could add a filter to each customer database to effectively exclude all the customer-specific objects. You can read about filters here
. This means you can safely get/commit objects and know they are just the shared ones (assuming you set it up correctly)
The downside of this of course, is setting up the filters requires some initial configuration (and possibly ongoing maintenance). Also, if there are dependencies between objects you're changing and the customer-specific ones, you may find that customer specific objects still get committed. You can turn off dependencies by editing the options
Hope that helps!