WP Super Cache should be safe to use and has been re-enabled. There was a bug that might have allowed the creation of directories outside the supercache directory but nothing more. That bug has been fixed. See Donncha’s official statement and Chris’s account of the bug and debugging process in more detail. Thanks, Donncha, for the speedy resolution of this issue!
I’m now testing the development version of WP Super Cache to help iron out the bugs. Pardon the dust. 
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I just came across disturbing “reports” of WP Super Cache being vulnerable to cross-site scripting code injection attacks. Just to be safe, I’ve disabled WP Super Cache and reverted to WP Cache v2.1.2 until the issue is resolved. Donncha is very responsive so I’m sure this scare will be behind us very soon.
Sources:
Donncha’s Thursday Links
wp-super-cache cached too far for me (and others)
wp-super-cache vulnerable to PHP Injection?
Caching is one of the most effective methods to reduce server load and improve load times on a WordPress site. There are two commonly cited caching methods one can utilize. Surprisingly, most guides recommending caching methods to improve WP performance do not mention the significant drawbacks. In fact, many common “guides” for increasing WP performance with caching and gzip compression may instead decrease your site’s performance. Continue reading ‘WordPress caching woes’