Yes, UIKit only became easily customisable in iOS 5 and the OP's app was written for iOS 3.
But even then you can port it to native UIKit (which is a good idea either way), and then make iOS 7 frameworks optional, and add a few UIAppearance calls for iOS 6. The last two pieces are extra effort that might not worth it for < 30% of your users, but it's still completely possible.
But even then you can port it to native UIKit (which is a good idea either way), and then make iOS 7 frameworks optional, and add a few UIAppearance calls for iOS 6. The last two pieces are extra effort that might not worth it for < 30% of your users, but it's still completely possible.