They are persecuted because it would be living and passionate Christianity instead of a birth and marriage ceremonial culture church controlled by a repressive government, similar to how China handles Christianity, persecute and suppress the committed Christians while giving the the people a government approved and connected version to handle the visuals and ceremonies to absorb the Christian impulses.
I will grant that there is plenty of nominal Christianity among the Orthodox— just as there is among all other Christian traditions— but there is also plenty of living and passionate Christianity as well. I know it from having had the opportunity to know many old-country Orthodox from all over the old Soviet bloc, especially a lot of the younger people. I know people who grew up in essentially a catacomb church in Albania. They are some of the most serious and devoted Christians I have ever met.
I would never idealize the religious situation in Russia. Some of what you said is true, but it is also much more complex than that.