I'm sorry to hear it caused problems. I think we can maybe make the behavior more intelligent, it should not delete longer running branches by default. We are very reluctant to add options to GitLab as detailed in point 11 of the acceptance criteria of our contributing guide https://gitlab.com/gitlab-org/gitlab-ce/blob/master/CONTRIBU...
But if we can't make the behavior more intelligent we will probably have to add an option.