Conquest can earn points other ways. There would be no one left to contest control of any landmasses, for instance. The point values for this scenerio are for this scenerio, not representative of what's going to be up there on every one of these I host.
Score for wonders is for building them. If they are later destroyed or captured, that has no bearing. I would think you're not likely to see them destroyed, the AI's are not big on razing wonders. Let's hope you aren't "so sad" as to lose control of wonders you build.
Good luck. And... don't forget to finish Epic One and write your report!