What are the access you are willing to give to this partial sysadmin ? Some of the permissions can be granted   by delegated development or application administration feature.ThanksShrity

Patrick,Any deletes doesn't gets propagated using App repo.   If that's what you are experiencing then it's behaving as designed. ThanksShrity

ATF is not limited to Global scope only. There is an outstanding PRB to address this problem. Will let you know once the fix is available. Stay tuned !!