It's my understanding that the Russian government really cracks down on any Church or organization that tries to proselytize people away from Eastern Orthodoxy. The Russian government only recognizes a handful of religions as "legitimate" apart from Orthodoxy - Islam, Judaism, Buddism, and perhaps Catholicism. I'm not sure about the standing of Lutheranism or any other Protestant faith.
It is my understanding that the pastor and local Orthodox Priest have an excellent relationship.
I think they are recognized, as they have permits to build and such.