This is the way I see it, Religion already has their hand in the tax payer's pockets.
There are tax exempt religions, individuals receive tax deductions for expenses at private religious schools and I am sure there are more examples.
If a Religion doesn't want to support health insurance because of a specific reason, then they shouldn't be accepting any sort of aid or help from the Government.
Just because health insurance could offer birth control doesn't mean anyone's congregation has to actually use it. And anyone arguing pregnancy is not a medical condition is just stupid.