Perhaps Obama will help close the “God gap” by his open hostility to religion . Smart atheists will see that if a president has the power to banish religion from the public square, some other president may have the power to impose religion on the public. If they value their freedom to not practice a faith, they should equally value the freedom of others to practice theirs.
The stance is pretty clear employees should expect the same basic health benefits across the board, independent of their employer. If you as a religious enterprise have secular employees, the just expectation is that you also extend to those same employees their secular rights under law.
There are also some sound policy reasons for that, but also back to your legitimate concern about justice, one of equity. If we allow this exclusion then in principle we have also allowed others to whittle away on the benefits they provide. Your position also makes sense were your starting assumption that health care is something voluntary in nature as opposed to something closer to a right.
Additional Note: There remains a searching for religious hostility on the part of the conservative Catholic wing, but I think that argument crosses a line with birth control. Whereas the Church’s objection to abortion is well understood and intuitive even for those who do not believe, the objections to birth control are simply harder to understand, underpinned as they are by the particular Catholic metaphysics. In fairness, Archbishop Dolan’s response on not medicalizing pregnancy was as sharp an approach as any I’ve seen. Would not surprise me if this became normative; the appeal to conscience, less so.