Quite a few civs have been eliminated from my game as well, but about 12 are still around (~6 major civs and 6 of the minor, non-playable factions).Fortunately, I haven't had any CTD issues in my game. I'm in the year AD 1966 now, and many civs have been eliminated from the game.
RE: the GPU... have you considered going into the NVIDIA Control Panel and adding the CIV4BTS executable to the list so you can manually override some graphic settings?
Also, if you're running Windows, you can go into the Graphics settings to ensure that the executable is using the GPU and not the integrated graphics chip.
Manually override which settings though?
I am running Windows and have disabled the integrated graphics / set the primary graphics output to PCI Express in the UEFI, however I've doubled checked and added the BtS.exe and the two manual choices were: optimized for performance: GeForce 1050Ti, or optimized for endurance: GeForce 1050Ti. So I'm pretty sure it's using the GeForce 1050Ti