Judicial immunity doesn't work like that. It protects judges from civil suits, particularly for slander, brought about through the course of their duties, but judges can face criminal charges just like anyone can. If the case against Taft was legally sufficient, there's no way the arraignment judge should have just thrown it out.
In the hospital when Det. Stabler takes the mother away, he tells her shes under arrest for the murder of her adoptive daughter. This should be attempted murder since the aunt took the biological daughter to say goodnight to the adoptive daughter. At that time, she is still alive.