Although hn doesn't have an exact assigned niche (it falls towards science and technology but that's not an enforced rule), it's fairly civil because the site doesn't need to make money and it's well moderated (almost to the point of authoritarianism, albeit that's not necessarily a bad thing in a website). A similar phenomona can be found in a place like r/neutralpolitics (heavily moderated to keep everyone on track, doesn't need to make money since subreddits are free).
This isn't feasible for a site the size of reddit though (they need money for servers and stuff), so federation is the only real alternative since each sub would pay (probably a provider, honestly, but they could selfhost) a little to keep their spot going. The trick is to make the federation invisible to the end user through some kind of reddit-ish frontpage site, which would be much like current reddit's frontpage but be accessing the federated subs, each with it's own moderators/janitors. This may be unfeasible, but it's the only way anything like reddit could keep free speech up. Add an easy to setup ad-network for each sub (they can opt-in to serve ads to the people accessing their sub's page, like Google ads on blogs) and it works. If a sub becomes evil just unsubscribe.
Avoiding eternal september sounds like a killer feature to me :P