Once target is on users, on human, technology could do just little help for it.It is confirmed that XcodeGhost will receive commands piggy-backed from the server response. It's capable to send harassment notifications and send URL request, which may lead to direct download of Apps built with enterprise certificate. Fortunately, these still request user interaction, and iOS 9 will show extra warnings and block these enterprise deployments by default.
However, the biggest risk is what you said: phishing.
Phishing attack is not limited to XcodeGhost, and iCloud is not the only target. There is no good way to stop these attacks other than passive blacklist, since it can't be caught by scanning codes. The message contents of notification dialog is not hard-coded but received over internet.
Apple could force fingerprints to be scanned by default for all kind of iCloud certifications. However, they still can't stop phishing attacks targeting different services, such as Battle.NET. Suppose that an contaminated 3rd party "Hearthstone Deck Simulator" app is asking for your Battle.NET account, will you ever be suspicious of it ?