I don't know if a shill-free alternative to Reddit could ever exist- I tend to think the openness and scale of Reddit (which is the whole point of it) is what allows shilling to occur. It really bums me out.
The site itself would have to be attempting to detect and flag networks of users, and take some kind of action.
Sure, but I think that is actually a very difficult problem: how do we determine whether a comment is being sincere or not? Furthermore, assuming we had a foolproof method to do this, would the site have enough funds to use it routinely and ethically? I think this is the problem we're seeing now with a large number of tech companies.