Best way to manage Source Control for Remote ASP.NET Websites & Services

We have a pretty complex set of Websites and Web Services on our staging and production machines. Right now, the devs use VS 2010 to remotely adjust the files on staging in real-time (I believe it automatically uses the frontpage synch extension, even though we don't technically use frontpage).

The problem is this creates an issue with source control with our subversion system. When the source is local, it's no problem to use Tortoise or a good VS2010 plugin; but my understanding is working via the remote file synch, there is no manageable file structure for Tortoise or the VS2010 plugins (unless somebody knows of a good source control tool which will work with the remote auto-synch).

Also, we're looking to upgrade to VS 2012 for the enhanced Azure support (we're migrating our staging area to a Azure VM).

So the question is how can we support the remote development of our staging systems (I'm talking direct file adjustment, not publication of packages) while also ensuring the remotely adjusted source is properly managed in our source control system?