I've always thought that they should kill off religious as the game goes on, and this may be a way to do it. Assume an 8 Civilization game. Six religions can be founded, first come first serve. Then when half of the Civs are in the Renaissance era, the smallest or least influential religion dies, and the most influential religion on the Holy city gets their pantheon. Then the same thing happens in the modern Era to bring it down to four.
I also think it would be cool to be able to use a GP in the atomic or info Era to create a secular state, which would wipe out your religion, make it extremely difficult for your people to convert to other religions, and convert all of your faith output into science.
Well I realise I'm potentially opening a can of worms here but personally I think it's a bit of a modernist/progressive/humanist fantasy that religion will die out. That idea was most popular particularly in marxist circles when religion was viewed as a tool by the Tsars & Monarchs etc to 'drug the masses'. These days It's only perceived that religion is dying in the West because western society has become very hedonistic, materialist and individualistic. And that is largely because much of western media, academia & bureaucracies is stacked with atheists/progressives/secularists that usually dictate popular debate, government policy etc, this does create a bit of group-think outlook where people have convinced themselves that religion will fade into insignificance. Just take a course in an arts or humanities degree at a western university to see what I mean
I think evidence has and is continuing to show the opposite. For instance after the USSR fell the resurgency that the Russian Orthodox Church experienced was very surprising considering the communist party spent decades trying to shut it down.
And to be honest communism and fascism (particuarly nazism) built a religion focused on 'Cult of Personality' as a means to control the masses... That basically was developing into an organized religion which tended to incorporate pagan festivals and other ideas like racial purity, the motherland etc..... So even the most avowed atheistic dicatorships (Nth Korea, Nazi Germany, Soviet Russia, Khmer Rouge etc) were building their own religion to control people, no different from what Marx was against.
In the west today. Europe may be very strongly secular and atheistic but America is still quite religious. And the West only encompasses a small proportion of the Worlds population. People still think of Rome or the USA as the centre of Christianity but today the demographic centre of the church is actually closer to Africa or China than to Europe or the USA.
The reality is that religion if anything is actually becoming more influential today (the West being the exception of course). Case in point is that nearly every day there is news about the rise of islamic fanaticism etc...
The issue of same-sex marriage also intertwines in this. It is often perceived as being a major human rights issue that has enormous popular backing but in reality it's only a handful of the most secular western countries (which in turn represent only a tiny minority of the human population) that is legalising same sex marriage. In Africa, Asia, the Middle East, Russia etc there is no or very little popular push towards same sex marriage as those regions are still either very religious or the culture is still very traditionally patriarchal.
The other point in regards to killing off religion (I think religion in Civ 5 is ok) but consider Judaism for a moment, it has less than 20 million adherants and is only a fraction of 1% of the human population but it still thrives and has a strong foundation that will allow to continue even though it has had the rockiest history of any religion.
If you wanted to have an option to get rid of religion than arguably it should be through the Order and Autocracy ideologies. Perhaps a Cult of personality policy (would remove the effect of religion in the city and provide a happiness/culture bonus instead). I'm sure those Parades that the North Koreans do can count as culture
Freedom/Rationalism does I guess reduce the effect of religion (as it co-incides with the rise of secularism) but by that stage of the game the effect of religion is pretty trivial anyway, it's usually a small amount of culture and happiness that you don't take much notice of, or the passive aquisition of faith to buy great people.
By the time you get ideologies religion is usually not something you're worrying about.