@lockeWiggins,
My understanding of the case is the father did have objections. Unfortunately he died in a motorcycle accident prior to this case so he couldn't be questioned.
She actually lost custody of the child to his father after doctors realized the boy was not taking medication. According to the report this was treatable lymphoma so neglicting the medication would cause death.
Also, recently, the state Supreme Judicial Court, determined in a previous case that parents have a legal duty to provide medical care for gravely ill children, regardless of religious faith.
According to the law (whether you agree with or not) in MA is should be guilty as she did not provide medical (and even in this case prevented) care for the child. The jurors actually said they did not want to say guilty, but under the law she was.