You are very right.

A YC Moderator responded to a similar post alleging that it was necessary to maintain civility. If someone reading this is a Moderator, I dare you to do a test. You have the resources. Select several hundred suppressed comments at random and tabulate wether there is abuse in the post, or if not then tabulate it as disagreement. This is the sort of thing you are paid to do, so do it!

As you say it's actually being used to suppress divergence of opinion. Every time it's done to me, it takes longer than before for me to resume commenting on HN. Eventually I will stop.

What can be done? Sufficient loss of reputation points for a down vote etc. would probably be enough to discourage frivolous actions.