By your own logic, this solution would take the democracy out of comment systems. Were News Genius to establish a “whitelist,” it would concentrate power among an upper-crust of news orgs; further, your “opt-in” commentariat anoints an unelected class of bloggers to represent the readership constituency. You trade the tyranny of the masses for the tyranny of an oligarchy. (You refer to these as “layers of community.”)
While you can conjure the pitfalls of that arrangement by yourself, I’d note that such an arrangement not only has a place in the media ecosystem, but also already exists in various forms (e.g. Flipboard, Apple News, Facebook Instant Articles).
You kind of dip into the ‘graffiti’ argument against digital annotation (i.e. strobe GIFs on the epilepsy site), but, frankly, annotation exists in many permutations… and has for many millennia. News Genius, social media, or even journalism itself are all iterations of the same concept: annotating original sources. In designing such comment systems, there are infinite potential combinations of all the sliding scales between each centralization & decentralization, scale & scope, anonymity & identity, censorship & anarchy, democracy & autocracy, crowdsourcing & curation, accessibility & exclusivity, etc.
Basically, stop worrying and learn to love (or leave) News Genius. I’m sure they want your feedback, and I’m sure they’ll iterate tirelessly to optimize the product. Genius will likely end-up occupying a unique niche of its own — one of the infinite possible combinations among comment systems’ various attributes.