When adults choose not to accept medical treatment because of their religious beliefs, and end up dying, no one really seems to care. I sure don't.
And I personally don't think the fact that a child was involved in this case makes it any different: we can't just go around taking away the children of people who have religious beliefs that reject what most consider to be conventional modern medicine. When you start making policy decisions based on religion, it's possible to quickly end up in a place that most of us don't want to go: why not just sterilize anyone who claims to be a Jehovah's Witness, or take away their children if they already have any. Extreme and offensive to the max, I know, but so is a parent actually letting their child die by choosing prayer over conventional medical treatment. The reason it makes news headlines is because it happens so rarely.
Freedom of any kind, religious or otherwise, has a price. And in cases where religion and medicine come into conflict, the price is a few unfortunate deaths that could have been otherwise easily prevented.