SO is an established site and nobody can earn these badges anymore. I understand why they are displayed in the list of badges. I myself visited AREA 51 to catch some aliens, oops see incubating sites.
What I propose is to mark these badges as Closed on SO. It will make it clear that it is not possible to earn them on SO anymore. There is already precedent:
Analytical - Visited every section of the FAQ (retired)
We can update badges description in similar way with (closed) suffix. It will not hurt anybody's feeling but it will help to clarify them.
This post is related to, but is not the same as, the following post:
I'm not suggesting these badges be removed from the list, merely that it be annotated in some way.
Please change Beta badge description to "Actively participated in the private beta for this site".