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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