You are right, Flipper - it is a difficult situation.
It is difficult to observe from the "outside", not only from the outside of the jworg but also from the outside of Russia.
Russia deals with terrorism in a way that we don't - their experience with a major terrorist event happened before America had to deal with it and not only that, but the countries where the seeds of that terrorist activity are born, butt right up against Russia - they are right next door and ever present. Russia shares borders with several volatile areas and those borders are permeable when "missionary" activity goes unchecked. Infiltration of established networked organizations is a very real threat.
Regardless of the JWs "neutral" stand, and regardless of how righteous individual congregations and JWs are, the way that their org is structured makes it very vulnerable to unknown terrorist elements. Unknown even to the JWs themselves. Combine that with the way that the org moves money around, and the entire structure of the JWs in Russia becomes not only suspect, but recognized as a vulnerable institution.
The JWs lack of awareness in today's terrorist climate is what gets them into trouble. It isn't the 50s or 60s or even the 80s anymore - it is the 21st century where we are dealing with different factors. The question that the org/JWs really should be asking is this - why does their organization fit the description of an organization that can be classified as "extreme"?
They have been labelled "extremist" but that is only because that label now exists in a legal context. They have always been extreme in their teachings and actions. Given the current climate, we have been conditioned to equate "extreme" with extreme violence but there are many forms of "extreme" that appear to be non-violent yet leave destruction and harm in their wake. The Watchtower Society is one of those apparent "benign" forces that leaves nothing but twisted and burned landscapes behind it.
And another thing...a comment or two about Chechnya. I have heard many reactions to "the gays in Chechnya" and equating the treatment of JWs to that situation.
Firstly - being gay isn't a "belief". That is obvious. And I am as much against the mistreatment of gay people as anyone is.
Secondly, the situation in Chechnya has context that should be considered. Russia barely, just barely, holds onto that tiger by a tenuous grip of its tail. The conflicts and tensions in that area go back centuries and it has only been recently that the full boil of war in Chechnya has lowered to a simmer. It was as recently as the 90s and early 2000s that war was active in that region - war between the Chechnyans and Russia. To hold Russia responsible for Chechnya's (97% Muslim population) treatment of people within its borders, and discuss it in relation to the ban on JWs, is unrealistic.