The code signature would no longer match after modifying a binary using lipo. So the bundle would need to be re-codesigned afterwards.
Apps built with Xcode 4.4 and even earlier will still run just fine on iOS 6 devices; and there are reports that Apple is still accepting apps built with the iOS 5.1 SDK.
Objective C will allow you to use some of the newer APIs not in the older linked frameworks via calling them thru the Objective C runtime by name. (Of course, the app should check for their availability on the current device first!)
You can even support the new iPhone 5 display from an earlier Xcode and pre-iOS-6 SDK by simply including a 568@2x tall Default image in the app bundle, and setting all your app's window and view sizes and resizing properties properly. UPDATE: Apple is no longer accepting apps built this way when submitted to the iTunes App store.
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Another potential solution is to split your development into two similar apps. One for iOS 4.3 and up. And one for iOS 4.2.x and lower with not iOS 6 and iPhone 5 support. Two different apps in the app store. However it is unknown whether Apple will allow this.
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