There’s definitely an argument to be made that the mutants should have the right to live their lives. I guess it depends on how much you think “violence” and “by any means necessary” are justified.
To bring a real world example into the conversation, the Palestinians decided that violence was necessary. Some condemn them for it, some ask “what other choice did they have?”
Obviously, the sympathizers will see you as the hero, and the opponents will see you as the villain. Is it better to go onto hiding like Prof. X and his crew or to stand up and fight like Magneto and his? And how much and what kind of collateral damage is acceptable? It’s a war that has been fought for ages in many different places - the battle between the oppressors and the oppressed.