They are already quite separated. It would be good if they were separated even further from my point of view (because the value of HN for me outweighs the value of YC tremendously), but since HN does not have a monetization strategy it currently needs support in the form of employees generously paid for by YC.

You'd need to at least begin to solve that problem before you can ask for more separation than there already is. And from a community perspective I think Daniel and others are doing a pretty good job at keeping an even keel when it comes to not giving YC preferential treatment. The only bit left is the job postings, which is probably a fair way to pay back for what YC does for HN.