Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereofFirst, since there is no enumerated power to the federal government with regard to abortion, states do have the right to decide the issue for themselves. I find the practice personally repulsive, but if I state wants to allow it or prohibit it, I recognize their right to do so and my right to live in a state whose laws are inconsistent with my personal views.
I have already posted elsewhere how I would handle same sex marriage in a way that would respect the rights of states, the neutrality of the federal government and protect the religious freedom of denominations that choose to allow it.
As to the separation clause, do you know where that appears in the Constitution? No where. However it does say, "Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof." Lets revisit abortion for a moment. You will find faith-base opposition to the practice from the Catholic Church, several baptist denominations, jews and muslims. Its a cross cultural value that isn't limited to an individual faith tradition or Church, so banning the practice has nothing to do with making "a law respecting an establishment of religion" or violating the separation clause.
What remains the same is that liberals are by and large ignorant about history, civics and law. They can serve up platitudes but can't expand upon them with any critical analysis.