»How does Mojang do this?

How can Mojang blacklist a server that's not in premium mode?
1. They don't have access to the computer / network of the server owner
2. Servers only use the minecraft website for skins and kicking anti-cracked players.

And they've still done it

 

Well, it is there game.
So when the server would upgrade to 1.9.3 it would get blacklisted meaning the IP is blocked pretty sure.

 

If you haven't already seen,here is the thread made by aXed:http://www.guildcraft.org/threads/mojang-eula-enforcement.19398/page-12#post-135261

 

They hard coded it right into the 1.9.3 version. So when you download that version the blacklist exists in the code. Just imagine every copy of 1.9.3 in the entire world has an encrypted link to guildcraft built right into it. With about 22 million copies of the pc version sold that's quite the honor.

 

Cracked launchers may not have the blacklist though.

 

dude srsly, go read the news and announcement
or better yet, do guildcraft.org and you will see it in the home SCREEN