Those comments with even an air of controversy will not be approved because if it ends up with down-votes, that will go toward the approving member's record and may end up getting them banned eventually.
Controversial points and less popular opinions and facts will never be seen to counter. PG, you are building a Censorship wall so that controversial or unpopular comments now don't even exist to refute/debate. There is a reason that anytime you take away people's free speech or expression, they eventually revolt.
Why do comments that are not mainstream have to go away (as in never be seen). Why not engage in debate about them. I never understood this. Sure I can see censoring comments containing personal threats or vulgar content, but this is ridiculous. Keeping information from someone's eyes just because one group does not agree with it is censorship.
Honestly, the way that disagreeable comments are handled now are quite refreshing and are one of the reasons that HN is so popular. Anyone can post their opinion. If people don't agree with it, they can engage in civil opposition. If it is inappropriate, they can down-vote.
Perhaps the biggest reason for not pending comments is that you are going to dramatically change what shows up here. You have members of one group (or classification if you will) who are very active and will all have 1000 points, this group now is the voice of HN. Those who post more occasionally, post late, or don't pad their numbers by replying to the hot thread (rather they create their own which drops 3/4 down the page) now have a limited voice. Other groups likely have many differing opinions than the over 1000 class, they now have no voice. You see, your over 1000 (certainly the minority of your members) mostly all have common opinions, ideologies and viewpoints about things. This group now has the power to silence those others (though perhaps even larger in numbers) groups.
I would have liked it if you ran a poll before coding something like this. A last minute pseudo-courtesy notification shows just how much HN is really all about you and does not really belong to the people who actually own it (the public). Without us, you've got and idle server. No stories posted, no comments, nothing. Your totalitarianism attitude put a bad taste in my mouth.