I sometimes think that we should have to sign a contract in order to have kids saying things like we will care for them as best we can, play with them five times a week (at least), make them eat their peas, and seek out modern medical care (or at least approved alternative medical care), etc. That way if people say they can't sign because they believe that their god Fluffybutt will heal their children, they can be prevented from ever having kids in the first place.
The problem is that we would end up in the same place we are already in: society as a whole deciding what is acceptable and then imposing that view onto everyone.
But at the end of the day, that is what a society is. You can't really avoid it. Some societies are more accepting of alternative beliefs. Others are rigid. All we can really do is try and create a system which attempts to balance individual rights with collective acceptability. We do that through our system of democracy which includes a system of checks and balances and a judicial system where we are tried by our peers.
In this case, the couple had already lost a child under similar circumstances a few years ago. The state by itself didn't step in and force anything on to them. It put them through the judicial system and had them tried by their peers (who found them guilty). They came out of that manslaughter verdict with probation and a future requirement to seek appropriate care for their other children.
I agree with the caution against state intrusion, but I would argue that the intrusiveness of the state was quite mild in this instance. Now that a second child has died, it seems reasonable to be more aggressive. The vast majority of society believes that if these parents had acted appropriately, those children would be alive. If this was some other form of negligence, say leaving a child in a car in summer,I don't think anyone would be arguing against state intrusion. Faith isn't (or shouldn't be) special permission to be negligent.
As for faith healing, well I think it is idiotic. Believing in prayer is one thing. Eschewing a specific set of tools and knowledge for no logical reason is just willful stupidity.