To the question, Yes, the European Court of Human Rights have the right to decide and to tell member states what to do. The member states must comply. There is no "what if they don't?", they must. The Court is the highest appeal court for all European nations, and organizations and individuals can appeal to it. If the appeal is allowed by the Court to be treated, the result is binding.
The French case is not on taxes as such, as claimed by some here, but on taxes placed on gifts. The French state claimed a 60 per cent tax on all gifts given for a number of years, and it should be noted that the WTB&TS was the only organization from which such taxes were claimed, so it was a clear cut case of trying to liquidate an organization. Whatever one might feel about such an attempt, the Court has now nullified the attempt. Last year, it was nullified, and the WTB&TS and the French state were asked to come together and discuss how the state should free the mortgages it had placed upon WTB&TS property (closing of brach office, convention halls and some Kingdom halls). The state refused to discuss, though, and therefore the Court now ordered it to follow the Court's decisions.