I do not know at what position you are in this organization. I also do not know if the organization has any genuine grievances of employees pending.
Presuming that it's a holy organization and union demands are ingenuine and illogical. In this case too, the company will support the Manager to file an FIR, a case once. Knowing how our system works (police, courts, labor officers...), the Manager will need to seek help from the police seeking security, file more FIRs, which is an uphill task. To motivate law enforcement agencies to work impartially for you, they need a motivating dose each time and every time. The law is blind; it takes time and long-drawn efforts to make it see the truth. By this time, the poor manager will be harassed enough as due to these, he will not be able to do justice with his main job. No commercial organization will support this futile battle for long. The Manager will slowly become prey not only to the union but also to the organization, as any commercial organization will remove such obstacles and compromise to avoid losing its commercial/monetary gains.
Also, when you say our own man involved with miscreants of the union, I think it's a highly irresponsible and demeaning comment about your own people. I think such an environment and inside feedback will further give them a feeling of insecurity and push them to be on the wrong side.
Instead, the organization should empathize with its own people. It must do introspection on what is breeding dissatisfaction and loss of faith in its system. Take corrective measures, create a positive environment, and instill a sense of confidence in its people. This will help bring a positive change in your situation. This will require patience, true commitment from management not in words but in actions. Mostly organizations falter here. The values that they preach and expect from employees they themselves do not practice. Employees clearly decipher this deception, and then a situation like yours starts.