It seems like a pretty reasonable suggestion that doesn't feel like a lot of work, but could potentially prevent an irreversible mistake.
The OP's main suggestion is along exactly those lines. It's actually less extreme, in some ways (see OP's "Lesson 1").
> What put me on the wrong path was an otherwise completely unrelated action: I had just done the same (i.e., hidden an empty README) on my personal profile by making jakubroztocil/jakubroztocil private.
> GitHub’s conceptual model treats users and organizations as very similar entities when it comes to profiles and repos. In this context, and since I just wanted to repeat the same benign action on our organization’s profile, my brain switched to auto-pilot mode.
> I didn’t realize at the moment there’s an inconsistency in the naming of this special repo containing profile READMEs and that it differs for users and organizations: name/name vs. name/.github.
> That’s why I proceeded to make httpie/httpie private instead of httpie/.github without realizing my mistake.
The main thing I really don't get is why it even needs to delete all the stars? It's not like they delete all comments/issues... by users who have been deleted. So why could they not simply make the star point to a "ghost repository"?