You have to realize two things:
1) this verdict is in the EU. The concept of free speech and freedom of religion does not exist anywhere in the EU. State religions de facto also still exist there. While we can debate the drawbacks of this, the State has decided it is in its best interest to tightly control the population with taxes and regulations.
2) disfellowshipping is a form of psychological abuse. If it were true that, as the WTBTS claims, that its members have the freedom of association, that would be one thing covered by freedom of religion. But we all know lives are tightly controlled by elders and the organization and its members cannot exit without fear of physical or psychological reprisals by other members at the direction of its leaders.
This would be similar to saying a victim has allowed their abuse by an abusive partner by staying in a relationship, even though it is true in certain cases the victim bears some responsibility of excusing behavior, it does not absolve the partner from further abuse.
I personally agree that the organization should be able to qualify its own religious tenets without interference, but it should not be blanket absolved from the results of those tenets which have often qualified the tests for incitement to violent behavior.