Yeah, if you're doing things that way, you have to set things up to be flexible. Have a flowchart ahead of time. (engineer your final event so that it can occur in a number of different cites, have special, minor events to step up difficulty in non-final cities that don't fall until finally the difficulty becomes too much, or just put the final event on the moon or somewhere else location independant, so it doesn't matter which city is the last one.)

Really just seems like a misstep. Sure, the Chinese overreact, but they do have a point in this case. Getting your players invested by having their actions change the outcome, and then railroading them is rarely a winning move. I thought Mass Effect taught us this years ago.