Hi there,
If you're getting that error message, then the updater was unpacked into the wrong directory. It needs to go into the base /Users/user/Library/Application Support/Steam/SteamApps/common/ai war fleet command/ folder, not into the /Users/user/Library/Application Support/Steam/SteamApps/common/ai war fleet command/RuntimeData/ subfolder, which is where it must be based on the error message.
Then once the updater is in the proper location, you should be all set! If it's not already downloaded the stuff into the updates folder (through launching it in-game), you'll need to do trigger the in-game download. But if it already went through all that, then all you have to do is just have the updater in the right folder and launch it like you were doing.
Hope that helps!