I'm not saying they are angels. They messed up badly at the beginning but they did it with good intentions and at the end the Progenitor took back all the murder and the damage it had done. At the end all the damage mutants suffered are due to Eternals and even then it's mostly Druig and his bs.
Edit: Oh and Progenitor was built to stop the war between mutants and eternals and it did exactly that at a crucial moment so..... mission accomplished?