I'd suggest something like a toast that says "4 new stories" and you click it to refresh. It means you don't get confused by stale data but the page stays under the users control. It also allows you to flag/highlight/animate the new stories so a user can understand the diff from when they last looked at the page.

This type of feature is sometimes implemented as a huge green banner stickied to the bottom of the view but that I find that too obtrusive and stress inducing - I end up clicking on them to get them out of the way even when I don't want to see the new stories so it actually makes the experience worse. I prefer a more subtle indicator in the top-right similar to how notifications appear in some apps but it shouldn't feel like an error/warning or something that requires immediate attention.

Love the project, thanks for putting it up.

The auto-refresh was making me crazy as well - even a big 'Auto-Refresh: ON' toggle by the menu would be enough.

I'm not a fan of settings in general but it does appear you're getting two distinct groups of users.

If you choose to have it as a setting, have a VERY big switch that stands out at the top, so people can SEE that it can be changed.

Then give the option to hide it, after you've made your selection. :)