It would be a pretty simple affair software wise, those that need it can have their safe space and those that don't can discuss whatever they want without being shouted down.
Seems like the optimal solution to me.
But if this "ignore flags" version of hackernews were to have any moderation at all to prevent the above, it would basically mean forcing extra work on the moderators of hackernews to cater to a handful of people interested in genuine discussion and a vast army of people interested in using it to troll, harass, and generally be awful to people.
I highly doubt that. Typically a normal discussion (such as this one) is underway and the suddenly the whole thing is killed. That's rude, to put it mildly and I see absolutely no harm in letting those discussions continue with the normal 'up/down' vote mechanism taking care of the moderation. Flagging just affects the ordering of the stories and does not have anything to do with the comments within those stories.
Note that there is no reason that you would not be able to discuss this site and yet the discussion is flagged so the majority of HN will never see it. I don't like that, I think it puts too much weight to the flags in relation to the upvotes.