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Re:This is a Facebook-free Zone by kabr on Saturday December 24, 2011 @02:09PM (#3389426)
One disadvantage is since the comments are inserted with Javascript, certain robots have a hard time parsing them.
Re:This is a Facebook-free Zone by Turing_Machine on Saturday December 24, 2011 @02:31PM (#3389472)
Other disadvantages:

You're handing over control of your user base to a third party. Some people don't like Disqus tracking them all over the web.