I don't know what the solution is. I wish I did. My point is simply that there is definitely a bias on HN, and I think few people would seriously claim that it's right-leaning.
A multi-axis perspective would probably be more useful: one could say that the pro-business/pro-startup bias is right-leaning, but one could also say that it's libertarian, and libertarianism isn't necessarily on the right when compared to "conservatism" or other supposedly "right-leaning" political views.
Regardless, from looking at the articles that make the front page, and from reading comments on stories that have a political slant (e.g. anything environment-related), what I see flagged and downvoted into obscurity--excluding obvious guidelines violations--are not left-leaning comments, but right-leaning ones, including many thoughtful, reasonable ones.
At the same time, trite, left-leaning, talking point-style comments remain at #000.
This is plain to any observer who's been here a while.
So I don't know the answer. However, maybe a first step would be acknowledgement. I would love to see you and/or other mods openly admit the left-leaning bias on HN. Not an admission of guilt on your part for supposedly moderating unfairly, but an admission that the output of the HN "program," as it were--which includes the community, not just the actual code and staff--is left-leaning.
If nothing else, perhaps it would help certain outstanding members of the community recognize the problem and be more open-minded. I don't think anyone benefits when good comments are shamed into obscurity and their writers are driven away. That doesn't help the problem of polarization that our society is facing.