Under the unusual make-up of the EPO, it has legal immunity from the laws of the countries in which it operatesThat is absolutely standard for international treaty organisations, which by their nature should not be subject to national laws. Most of them, however, set a standard of 'not worse than the host state law' when it comes to health & safety, employee rights, etc. It doesn't sound as though the EPO is doing that.
On the other hand, Philip Cordery is a socialist so he would be expected to take the employees' side. He's also half-British (not that that counts for much in Europe these days) and represents non-resident citizens. In fact he represents some of the EPO employees directly, since his constituency is "les Français du Benelux".