I'm also playing Beyond the Sword. I decided to start over using some of the strategy information I've gleaned from the CivFanatics forums. I'm building my new civ around one very basic concept, technological elitists. I do not deal with any of the other "lesser" civs except to destroy them should they arise my ire or to steal pitiful technologies that aren't worth my civ's time to research. I've never taken on a state religion or built a religious building. It's research, money, or military.
I realized pretty early on that I needed some breathing room. So I did an America. I conquered every last Native American city and took their land. All of it. The Mongolians weren't happy with this so they declared war on me. They never bothered attacking, of course. I was able to take 4 or 5 Native American cities while the Mongolians just spewed insults and called me backstabbing, blah blah blah. I've rejected every single trade and open borders proposal I've ever gotten. After taking all NA cities, I moved to assault the Mongolians. And I was wading deep. I took one city (which will probably flip back to them soon unless I can do something), but could not break the next. So, I offered a Peace Treaty. They accepted.
Now that I'm out of war, I should have no problem getting my research back to its top levels. And maybe enhancing my espionage as well. I have every resource I could need so far, so my isolationism should be fine. My overall plan is to build up to the Manhatten Project. I'll stockpile nukes like there's no tomorrow and hope that's a heavy deterrent. If that doesn't work, well I will have no qualm about unleashing armaggedon. Assuming I can get access to Uranium. This is all to keep the idiot civs from raiding my cities while my people work towards travelling to Alpha Centauri, where we can research more in peace!