I think that publishing a protocol is an interesting idea, but the entropy afforded by the current system seems to work well for HN. If anything, I could potentially see mentioning that people should probably not downmod just based on personal opinions.
The problem is that the big Hacker News personality type is one that gets very intent about arguments. I absolutely do. And when you're in an argument, even if you think the response is intelligent and contributes there's a kneejerk desire to downvote and hope that the hive mind will follow you and downvote. I'll admit that I've done the same, on occasion: it's a very pervasive mentality.
It helps not being able to downvote until you have a certain amount of karma: it gives you a period of time during which you need to learn to respond intelligently. But that isn't an entire fix to the problem. Thankfully, to date it's still the uncommon thing to happen.
But having it said officially probably would not hurt the situation. I agree, though, that things rarely get out of hand - why I love HN.
I naively assume (hope?) that all discussion will be intelligent, so I don't see any need to reward it. Consequently, I rarely give or take points away from a post.
edit: I do rarely updmod posts I disagree with if I feel they are valid, and have been unfarily downmodded. I do this out of a desire for fairness.