I think that most people use default settings, so this system would work best on a site where this would be the default setting.

I think this is a minor convenience at best; when you choose to form your darknet, you could simply inform the other candidates of your plan: via email, PM, or some other out-of-band channel.

It would be interesting to find a good algorithm, which would have the following data on input...

This sounds pretty similar to Google's PageRank, only for comments instead of pages. Should be doable.

If the site is visible for anonymous readers, a global karma is necessary.

Yes, of course. The goal is not to turn the entire site exclusively into your darknet, but to allow you to run your darknet in parallel with the normal site as seen by everyone else.

I also wouldn't like to be shielded from disagreeing opinions. I want to be shielded from stupidity and offensiveness, to protect my emotions. Also, because my time is limited, I want to be shielded from noise. No algorithm will be perfect in filtering out the noise and not filtering out the disagreement.

Agreed; if you could figure out a perfect filtering algorithm, you would end up implementing an Oracle-grade AI, and then we'd have a whole lot of other problems to worry about :-)

That said, I personally tend to distrust my emotions. I'd rather take an emotional hit, than risk missing some important point just because it makes me feel bad; thus, I wouldn't want to join a darknet such as yours. That's just me though, your experience is probably different.