The factory exhaust is not put together like the aftermarket cat-back systems are it is only bolted on at the flex pipe the rest is fully welded and installed before the rear sub-frame is installed at the factory, so therefore the only way to remove it is cut it or drop the rear sub-frame.
You could always get your factory welded where you cut it if you ever want to put it back on. But the FSWerks exhaust is very simple to install I have not seen one post about pieces missing or anything like that. I would say go with the FSWerks.
Build Thread: http://www.focusfanatics.com/forum/showthread.php?t=321737
Build Thread: Already Built... For Now