Strictly speaking, only 'persons' can be excommunicated, since it is a process of excluding someone from the communion of the church. The understanding of this changed in Roman Catholic Canon Law in 1983, but not in a way that affects your question. Historically excommunication has applied, rather infrequently, to groups of people, but never so far as I can tell to an 'organisation' or impersonal structure. Examples of excommunication of groups includes for example, those involved in the creation of the Philippine Independent Church in 1902. This would be an instance of 'group excommunication', but it is still of persons, not of an organisation per se. The excommunication was carried out by the Archbishop of Manila under instruction from Leo XIII.