Rabbi Goldschmidt, threat to Russia's national security?

JTA is reporting (in its breaking news -- could JTA actually be reporting a story before everyone else?) that Russia's internal affairs ministry has confirmed that it will not be letting Moscow's chief rabbi, Pinchas Goldschmidt, back into the country. This is despite the fact that the Russian foreign minister recently promised Silvan Shalom that the matter would be resolved satisfactorily, and despite the fact that the man widely assumed to be behind the ban, Russian Jewish Congress head Vladimir Slutsker, resigned his post.
As you will recall, Moscow's initial excuse for denying Goldschmidt re-entry into the country was that his visa had expired. The strangest-sounding thing about the newest twist in the story is Moscow's new excuse:

The letter cited an article in Russian legislation that prevents foreigners who are deemed threats to Russian national security from entering the country.

Huh?
Apparently, however, this is Russia's normal excuse when denying religious figures visas. The majority of the references to this online are connected to a draft government report from 2003 which explicitely named the Catholic church, the protestants, the Muslims and a few sects as 'threats to national security' due to their 'extremism,' and outlined ways to 'deal' with them. I don't know what happened to the report -- I'm sure one of our readers will be able to tell us -- however,

The draft paper defines “extremists” as those who conduct the “propaganda of exclusivity, of the supremacy or inferiority of citizens according to their attitude to religion and according to what social, racial, ethnic or linguistic group they belong.”

These are the kinds of charges that were very recently made in Russia against the Kitzur Shulchan Aruch, which, Russian nationalists were claiming, was a racist document.
In any case, this article from 2003 quotes one Nadeshda Kevorkova -- I don't know who she is -- as writing in the Gazeta newspaper, prophetically, as it turns out:

“The officials have set down Catholics, Protestants, sectarians and foreigners as extremists — that is, everyone except Orthodox adherents, Buddhists, and for the time being, Jews."

Well, that was then. Russia already has a rather heavy track-record either expelling or denying visas to Catholic, Protestant and other religious leaders in recent years (using the 'national security' excuse). It appears as if this is finally the context in which we have to see its treatment of Rabbi Goldschmidt; this is not a Russian war on one specific man or organization but on religion, specifically non-Orthodox religion, which is being portrayed as un-patriotic, 'foreign' and downright treacherous. Suspicion of the foreigner and of the enemy within, of course, keeps Russian nationalism burning and shores up support for the government.
The question remains, however, what made them decide to turn the screws on the Jews at this specific moment, after years of 'protecting' them from these expulsions which affected everyone else (of-course, Putin always interfered in the Jewish community in other ways, but anyway). Had our luck just simply run out? Or, after all the speculation and the conspiracy theories, is there still more behind this story?

UPDATE: Shmarya's take here.