“How can it be a chilul hashem to ease the plight of agunos???”
“How does the valid goal remove chillul Hashem?”
According to the halachic definition of chillul Hashem, if something is a Mitzvah, it can’t be a chillul Hashem. Actually, it is a Kiddush Hashem, even if (maybe especially if) others look down on you for it.