I was concerned with the idea of site-wide pending comments, as it could have a chilling effect on controversial ideas, and water down discussions. Or, worse, eliminate comments past the front page, as no one would want to risk being blocked from further commenting.
You could alleviate the problem by allowing people to delete pending comments, but it's like asking people to sacrifice their own creations. It would make me think twice before spending time to comment next time.
Having this disabled by default, and enabling only on particularly controversial threads (that tend to bring the majority of low-quality comments) solves most of these problems.
I think this is the best approach. A good balance between negative flagging, and positive endorsement.
