If missionaries will request a great temple, it means that smaller civilizations will not be able to spread a religion.
This is a good point, but smaller civilizations can still adopt Organised Religion. Because they are so small, it shouldn't take them long to build all available flavours of Missionaries to evangelise all their own cities, and perhaps it is appropriate that small civilizations must run Organised Religion to be able to evangelise other civilizations.
Great Temples also remain extreamly rare untill the Medieval Era, in most games.
Not when I'm playing!

That's perhaps an instance of observational bias:
http://en.wikipedia.org/wiki/Experimenter's_bias
The idea of religions disappearing from the world is too evil.
And it does not seem to be true at all.
about 80% of the western world citizens believe in god, and more than a half realy follow the religion in many ways.
This is the difference between being a general theist and a member of an organised religion. Many non-atheists in modern societies remain theists but are agnostic about the
nature of God, so are not members of nameable religions, and perhaps describe themselves as "spiritual but not religious". These are often people who have abandoned the religion of their parents --- genuine atheists arise in numbers a generation later. Modern societies have created the social circumstances where this is possible on a scale undreamt of 200 years ago: When the social forces that compel people to remain members of organised religions (in particular family pressure and indoctrination in schools) become weaker, people who have the right to choose to walk away from the religion of their parents do so, and they rarely return or choose another religion. John Lennon was famously wrong about
how fast this effect was --- sometime around 1970 he claimed that by the year 2000 Christianity would be irrelevant. (Can anyone make this statement precise?).
I'll concede that the effect under Judaism is weaker, but Judaism is a rare combination of tribal/national identity and organised religion. (No offence intended!)
In contrast, there is currently a lot less evidence for the Star Trek notion that nationalism and ethnic identity will evaporate by ~2400CE through merging.
Maybe your can make the diplomatic effect of religions disappear in the Future Era.
This could only apply between two Civilizations both in the Future Era. As it is in the real world, Civilizations can live in different Eras at the same moment in time. Currently, a Civilization can choose Free Religion, but their neighbours who have state religions will still pressure them to choose a religion to ensure alliances in one direction or another.