Overall it's pretty painless, and the dormant users are thankful for the notification.
Shouldn't have been considered inactive.
In cases where an account does have repositories (user initiated renames) the old URLs/repos will redirect as long as another user doesn't take the old name and create repos with the same name[1].
[1] https://help.github.com/articles/what-happens-when-i-change-...
For both Gemfiles and submodules this is an extra reason to fork the original and reference your fork rather than directly link to the original (unless it is big and reliable and unlikely to to be replaced e.g. rails).
The update which came after your post says this however: "Our only guess is that she did not post as often as they might not have liked."
But he does say elsewhere that she used it often to rate images. https://news.ycombinator.com/item?id=7599802
Just nabbed https://github.com/stephen was inactive since 2008.
https://help.github.com/articles/name-squatting-policy
(And they should, I think.)
Since at least 2012 Instagram has had this in their terms:
> 4. We reserve the right to force forfeiture of any username that becomes inactive, violates trademark, or may mislead other users.
So whine about the policy if you don't like it, but don't whine that Instagram has materially changed.