it's probably better to just block all new users from downvoting. This way you teach the new users for 3-4 months, and they get ingrained not to go look for the downvote button every time they read a comment they disagree with.
reddit is general purpose, you can collect points merely by posting pictures of kitties or nsfw.
I think that explains why some are members for 2 years, comfortable in reading the content on the site and contributing rather rarely when they have something insightful to say, while others are able to reach the threshold for down-voting in short periods of time without fully understanding the community or reading the guidelines.
I'm assuming you got down voted because it's just a flat karma value (I guess 200?) to allow down votes. They meant that your karma from submissions shouldn't count because it's trivially obtained.
Edit: Thanks for down voting this.
If karma comes only from useful comments then I'd posit that the user will be more invested in discusion and not as likely to down vote others.
My point is if you remove karma for submitted stories you only get people who earned the right to downvote via well thought out comments.
My hypothesis is that these are the type of people who are more likely to counter a point they disagree with, with a well thought out comment, rather than a downvote, as that's how they got the karma they have to begin with.
Perhaps stories that make the front page for X amount of time should earn a standard rate of karma for the submitter. Or even just a limit, say you can't get more then 10 karma on a submission.
Social conscience++
Say HN gets an influx of new users who typically upvote inflammatory or LOL-evoking one-liners. If they all upvote each other, they all get karma, and the community starts to shift towards that behavior (because that's what earns you karma, and karma is supposed to be indicative of your contribution to the community).
I know I lurked here for about 6-8 months before creating an account and that time period allowed me to appreciate HN's community and what was and was not acceptable. Of course new members could still post comments and submit articles -- they just wouldn't have the ability to decide the community ethos.