The good news is that this is really easily fixed. The author of WeakAuras stepped in within hours of hearing about this with a modification to the code. Before performing either of these steps it's worth creating a backup copy of your Interface and WTF folders so that if something does go wrong you don't lose all your auras.
If you use the Curse client, all you need to do is uninstall WeakAuras, and install WeakAuras 2. Ensure that when you uninstall WeakAuras you uncheck the box that removes your in-game variables, and you're done. If you want to do it manually, head over to the download page, download it and merge the folders.
Simply log into the game and load up WeakAuras with the same commands as before, and you're done. Also, while this is fixed, a good general rule for WoW and the rest of the internet is this: don't click links from strangers.