It sounds like what you want to do can be achieved from git v2.13 on with the new --recurse-submodules option of git checkout. From the git-checkout manual page:
--[no-]recurse-submodules
Using --recurse-submodules will update the content of all initialized submodules according to the commit recorded in the superproject. If local modifications in a submodule would be overwritten the checkout will fail unless -f is used. If nothing (or --no-recurse-submodules) is used, the work trees of submodules will not be updated.
See also this relevant git mailing list message about that new option.
