Would it be possible to force Wonders in Gods of Old to be godly-power immune? All of the ancient wonders are pretty much decimated in the early-game by judicious use of Great Prophets calling down meteor strikes or tsunami waves. I tried looking into the Python code but I couldn't find anything about making buildings immune or which buildings are effected. The XML "nuke immune" tag only applies to nuclear weapons, not pestilent winds of doom.

Well the lines you want to edit would be (in CvEventManager.py):
if iBuilding != CvUtil.findInfoTypeNum(gc.getBuildingInfo, gc.getNumBuildingInfos(), "BUILDING_PALACE"):

since I haven't programmed in python I can't really say what that line should be changed to.