I agree that government shouldn't tell people how to live unless it directly affects the liberty of another. Utopianism is not something I'm interested in attempting. People are and should be free to choose how they want to live, but that doesn't mean the rest of us have to throw out our morals and religion in the public square to appease your choices.
Separation of church and state is not in the Declaration or the Constitution anywhere. It's from one letter from Jefferson. That's not binding law. Now,"Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof" is in the Constitution, but it's intent was clearly noted by it's authors to prohibit Congress from legislating either to establish a national religion or to disestablish a state religion. That's right, state religions are permissible. Just not national. Regardless, it doesn't mean what you and many might think it means. Jefferson's belief in a separation of church and state was not intended to create a safe space for everyone to be shielded from exposure to common religion in public, but rather a cautionary tool to keep government from taking over large religious institutions for their own self serving agendas like King Henry VIII and the Church of England thereafter or from squeezing out other competing denominations (ie protestants vs catholics).
There are some tough choices we have to make as a people regarding some of these moral gray areas like those you've listed, but for me it's fairly cut and dry.
For me, a fetus is a baby. If I kick your pregnant wife in the stomach it would kill your baby, not your "mass of tissue" that fetuses are made out to be. There are living botched abortion human beings walking around right now that prove that. Now a three day old fertilized egg may not have all the developed features of a human being, but we all darn well know that's what's in there. A living, growing human being. Our Constitution demands that we protect life. No one disputes that. A baby and/or a fetus qualifies as human life for me. We protect turtle eggs and eagle eggs as if they are the actual animal so why not human beings? Now, all that said, I believe certain medical conditions and extreme circumstances can permit the RARE use of abortion, but I don't think it should be used as a form of birth control as 99% of abortions are. Abortion was actually started as a mainstream practice by racist eugenics advocates like Margaret Sanger to control and ultimately eliminate the black population in America. Disgusting stuff. Nevertheless, thanks to a weird Supreme Court ruling it's a protected act. It should have been left to the states to decide individually as prescribed in the Constitution.
Gay marriage is settled. Just like abortion, SCOTUS should have simply allowed states to individually decide as prescribed in the Constitution. What they did was wrong. They have no business monkeying around in affairs reserved for the several states.
"The powers delegated to the federal government are few and defined. Those which are to remain in the state governments are numerous and indefinite. The former will be exercised principally on external objects such as war, peace, negotiation, and foreign commerce. The powers reserved to the several states will extend to all the objects which, in the ordinary course of affairs, concern the lives, liberties, and properties of the people." - James Madison.
That's pretty clear to me. From a Constitutional standpoint the gay marriage ruling is 100% wrong, morals aside.
Now as to the moral side of it, the Bible is clear. Homosexuality is a major sin. It's consistently referred to as an abomination and even had two cities famously destroyed. There's no question that according to the Bible which is the only source we have been given on Earth for God's word that homosexuality is a big no no. I do not believe that means we are supposed to mistreat homosexuals in any way whatsoever. I love gay people with all my heart. I'd help a gay person the same as any other human being. I just can't condone their lifestyle choice. That means I cannot agree with gay marriage even though I really don't care what gay people do.
I do not think marriage is something that was previously exclusionary toward gay people in the first place which was the only argument. Marriage is a religious act recognized by the state to promote the family unit which is the basis of our entire society, and by definition it is a religious ceremony proclaiming a mutual life time commitment between one man and one woman. Gay people were free to marry any non blood relative member of the opposite sex the same as everybody else. Conversely, they were also free to have same sex weddings in public all day every day without any persecution whatsoever. They just weren't recognized by the federal government or forced to be recognized by every other state. Today's gay activism's goal isn't tolerance anymore. It's promotion. But I digress. Had SCOTUS simply allowed states to decide individually as the Constitution prescribes we'd not have much controversy as the system would work like it was designed to.