Does religion expose the shortcomings of empathy based moral systems

[Whateverist]

No.

We all create theories, conscious or unconscious, about what reality is, how it works, and what the underlying picture really is.  Moral systems -- all moral systems -- are layered on top of these theories and interpreted through them.  Just as the meaning of a mathematical theorem depends upon the definition of its terms, and a sentence depends upon the meaning of individual words, so too, moral theories depend upon metaphysical and naturalistic assumptions.  Our morals are built out of these underlying theoretical assumptions.  A world that contains a God who is an embodiment of the good is going to inspire a different set of morals than a world which contains no god.  It is the underlying worldviews which are constraining the nature of the resultant moral systems; not any defect in sourcing morals to empathy.  My empathy is always going to be framed by what I view as the truth about the world, whether that truth is religious or not.  So no, religion doesn't expose any such shortcomings, or, if it does, it exposes them as being shortcomings which all moral systems share, namely a dependence upon the physical and metaphysical views of the holder for the ultimate content of those moral systems.

But I think you would agree that a metaphysical assessment which leads a person to distrust their empathic responses would be a detriment, as I think Christianity largely does.

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I'd say that religious belief exploits empathy to counterproductive ends, personally.  Religion works on and because of that stuff, not against it or in spite of it.

It circumscribes what you are to be empathetic about and how your empathy is to manifest itself.

I still think that by positing a higher moral authority, Christianity leads to alienation. Not that they can't be good people or happy, but I personally wouldn't want what they're having.

"If there is no god....what happens to the evildooers who get away, wheres the justice?"

The same thing that happens to them under Christianity, nothing, as opposed to what they imagine happens to them.