Resolving hosts from .ssh/config file in git plugin

We are using hosts in the .ssh/config file to set identity files for our remotes.  For instance a .ssh/config would look something like this:

Host homer-at-foo
       Hostname foo.bar.com
       User homer
       IdentityFile ~/.ssh/homer-at-foo.pub

TeamCity appears to honor this during the actual clone/pull of source when running a build but when doing things such as checking for changes, testing the connection for the VCS root and looking up submodule information. This is a problem for us because all of our submodules point through the host aliases found in the conf.  Has anybody found a way around this?