In GitLab 10.7 we added branch unprotecting restrictions that can be managed through the API to restrict who can modify protected branch rules https://docs.gitlab.com/ee/api/protected_branches.html#prote..., and we'll be adding a UI to manage this soon too. I created https://gitlab.com/gitlab-org/gitlab-ce/issues/49513 to add an auth step for changing protected branches as well.
I'm interested to know more about the version number improvement you suggest too. There are a few similar proposals like automated tagging on merge https://gitlab.com/gitlab-org/gitlab-ce/issues/22363.