Compare disfellowshipping someone to a jail sentence: the DF'ed person is free to move about as he pleases, but his friends and family cannot speak to him, lest they also be DF'ed. The jailed person is not free to move about as he pleases, but his friends and family can continue to have contact with him, without adverse risk.
Compare shunning to a restraining order: a restraining order can be requested by a person who feels threatened by another and seeks a legal ruling to force that person to stay outside of a proscribed distance, or avoid certain methods of interaction. Shunning is mandated by an organization, is not done at the request of an individual, and cannot be rescinded by anyone but the organization.
If the government of the Netherlands had never allowed clergy to sign marriage licenses and had not agreed to subsidize religions with an annual stipend, JWs would still be able to practice their religion, including the ability to disfellowship and shun their members. As the WTS claims to be no part of this world, they should not really have an issue with this ruling, and should hold it up as an example of how they remain separate from the world unlike other religious organizations.