Well, depending on exactly how much this blocks, this could get pretty awkward -- typing 'git log' in a repo owned by someone else can be awfully handy, even if file system permissions block changing it at all, and putting together a list of all places you might want to do this in advance could get pretty awkward. (Not running hooks, or allowing operations that would trigger them, from non-owned directories would preserve some of this usage, and still at least mitigate the dangerous cases somewhat.)

It's also not entirely clear to me what this does to site-wide shared remotes, though I suppose if they can be listed in system config, it's at least not a per-user hassle.