I tried using scm-manager for a few days, as an experiment more than a long-term transition from my previous server. Upon migrating back to my old server I noticed that "hg push" was failing across all repositories. I tracked this back to: https://groups.google.com/forum/#!topic/scmmanager/j-Q31vaShEc
I understand why you are adding the hooks, but I think it would help if you would add comments around the hooks indicating that they are only meant to be used with scm-manager and should be disabled when using a different server. Bonus points for automatically removing these lines when scm-manager is uninstalled.