1. You don't like to prevent religion from spreading, it's just a byproduct of theocracy. The benefits of that civic are too great to not have a detriment to it. If you planning on staying in theocracy then it's not an issue until the UN vote for worldwide Free Religion - which may not even happen. In other words, it's not that you don't want religion to spread, it's just that it won't spread. Your government is based on one specific religion and the other religions are effectively outlawed. But at two experience points for each new unit it can be worth it whereby Pacifism effectively limits the size of your military or your tech, depending on your percentages.
2. You can absolutely spread your state religion to both your cities that aren't yet of that religion, and to cities outside of your civilization. I believe that if you have a state religion you can only build missionaries of that religion, even if you have a monastary to another religion. No proof of that, but it seems to make sense.
3. Religions don't really work that way. The religion itself means nothing unless you have a state religion. You can build a hindu temple in one city and a Jewish one in another. They do the same thing, and I believe that your Jewish temple will still be effective even if you choose a different state religion later, but don't quote me on that. Therefore, religions do not take over cities. You get no penalty for having or not having a specific religion. That is, unless you have a state religion whereby that city without the state religion will not reap the benefits of having a state religion, even if it has all six of the other religions. Even when you pick a state religion the religions that were there before will remain, but you cannot build temples to them and cannot build missionaries to them. When you go to free religion later on you can start building those temples again.
[edit] Religions are not assigned to cities. Think of them as colors. I'm picking the blue color as my state religion - this city has red and yellow, but not blue, so I need to send a blue missionary there. If it's there you're covered.
Without this next part religions are more or less meaningless. If you are the first to discover a religion one of your cities gets that religious symbol with a gold star on it. Later you probably will get a Great Person in the form of a prophet. Send that prophet to the religious star city and build that religion's shrine. You get a big boost from that alone, but it gets better. After doing that spread that religion throughout the world as much as you can. Send your missionaries to different countries. Every city in the world that has that religion will then pay a tithe to you. PLUS you get to see into that city, as well.