Perhaps you should consider gitslave as an alternative to git-submodule, depending on your development workflow it may be better (or worse). Specifically to your issue, gitslave keeps all members of the superproject on the same branch (absent specific git (not gitslave) commands to do otherwise, and even then many commands warn you when you are on different branches).
Gitslave is useful when you control and develop on the subprojects at more of less the same time as the superproject, and furthermore when you typically want to tag, branch, push, pull, etc all repositories at the same time.
git-submodule is better when you do not control the subprojects or more specifically wish to fix the subproject at a specific revision even as the subproject changes.