For one, I understand completely how far they go. The freedom to practice religion is well established in this nation. And it is protected from active oppression. You're talking about protecting organizations from providing vital services to constituents under the religious organizations. These rights conflict. It's clear which ones win out. If they don't provide vital medical services, they don't have a place dealing with medical services. Also, the Tenth Amendment is the matter of rights reserved to the state and the individual, when the federal government is not directly given powers.
However, the medical well being of the nation is an implied power. (I'll take it you've heard of necessary and proper?) These services most definitely fit in here. I'm truly sorry you're so frightened of federal power you let a few butt hurt Christian institutions who don't want to give money for vital medical services dictate your definition of perfect examples of violation of the Constitution.