I'm (non-religious) conservative and I think the decision is wrong. A graduation ceremony in a church is no more a religious event than a graduation ceremony on a football field is an athletic event. It's just a building.
If people are up there preaching religion instead of reading the graduates' names like they're supposed to at a graduation, that's one thing. But what the building is normally used for is not the same thing as what the building is currently being used for. If it still has a huge crucifix above the podium, and you can still see St. Peter in the stained glass windows, so what? That would not be an example of government forcing religion on anyone. Freedom of religion does not mean freedom from religion.
I've also believed for a long time that there is nothing unconstitutional about displaying the Ten Commandments in court rooms etc., as long as the law of the land is what's being enforced and not the (supposed) law of God.