I don't think I would frame that as a flaw of having a voting system at all, which seems to be what you are saying. HN also has a voting system, which, overall, I quite like. It helps that on HN you have to earn the right to downvote. You have to work for it.
There are plenty of longstanding accounts on HN which have not passed the karma threshold for getting the ability to downvote. Those people not willing and able to put the work in here are denied the ability to just driveby downvote out of crabbiness. Those invested enough in the community to have earned the right to downvote are more willing and able to use it responsibly and not just as a means to vent their momentary negative feeling.
I think the Reddit problem is a problem of culture, compounded by the human tendencies to a) express emotion more than real thought and b) take the easiest way out available. You can downvote from the get go on Reddit. I think that promotes a negative atmosphere because people not yet invested in the community are free to use downvotes to basically piss and moan. The minority that does care or know better gets drowned out. The negativity becomes intractable.
On HN, you are unlikely to earn enough karma to downvote if all you ever do is piss and moan. The quality of conversation here is rigorous enough that if you have the ability to downvote, odds are good that you either already knew better or grew enough from interacting here to not routinely and consistently just piss on people for momentary gratification.
The ability to voice meaty reasons behind disagreement, and do so in a genuinely respectful manner, is one of the strengths of HN. It has been weakened but is not dead. That particular strength can be shored up here. I have not heard anything to suggest that Reddit ever had that. From what I know, introducing something like that to Reddit would amount to a disruption of what Reddit currently is and always has been.
It is that meatier discourse which makes disagreements or differing points of view a real asset for a community rather than just a source of negative emotion or lurid entertainment. HN still fosters that meatier discourse, though somewhat less well than it once did. I have not heard or seen anything which suggests Reddit ever had that.