Beyond being a terrible personal tragedy, the murder of Mary demonstrates Michael's hypocrisy and ultimate failure. He justifies everything by saying he needed to protect his family. But he's lost almost everyone and, in the process of trying to get them back, loses his most beloved family member forever.
It was put perfectly, and pithily at the beginning of III. Michael shouts at Kay, "I protected my family from the horrors of this world." And she replies, mildly but firmly, "But you became
my horror."
