My master branch layout is like this:
/ <-- top level
/client <-- desktop client source files
/server
There is a solution. Grab crdlo's patch for capistrano and the capistrano source from github. Remove your existing capistrano gem, appy the patch, setup.rb install, and then you can use his very simple configuration line set :project, "mysubdirectory" to set a subdirectory.
The only gotcha is that apparently github doesn't "support the archive command" ... at least when he wrote it. I'm using my own private git repo over svn and it works fine, I haven't tried it with github but I imagine if enough people complain they'll add that feature.
Also see if you can get capistrano authors to add this feature into cap at the relevant bug.