The European legislation regarding ATC principally covers the provision of services to GAT within airspace that is the responsibility of a Member State. In broad terms, the European Commission does not have legal competence over military matters and so in most cases the rules do not directly apply to military services - however, the Member States are supposed to seek the same standards from their military in certain specific situations.
If the aircraft receiving the service from the carrier are OAT you probably don't need to worry about EU legislation (some may choose to interpret a few bits of the legislation it a way that includes your ops but the European Commission has bigger things to worry about!). OTH, if the aircraft are GAT (or the movements are predominately GAT) and the carrier is within 'European' airspace then the rules probably do apply where an ATC service is being provided.