The thing is EFF article heading is misleading. These listed websites are not "major independent news sites". And they never been. When it comes to independent news sources, Russia uses a lot of newsru.com, lenta.ru, utro.ru, none of those blocked. Besides livejournal.com works from Russia as usual. Serve it from open public proxy in Novosibirsk and see for yourself.
It is sad EFF became a channel for demonization of Russian public image these days.