I have the same problem - no need for the iPad version and Apple reviewers rejecting the app due to scaled screen appearance on that device. I want to remove the iPad capability in my app, but Apple is not letting me to do that. After unchecking iPad option in Xcode, when using Archive to send the app to Apple, I get an error and a pointer to this app note:
https://developer.apple.com/library/ios/#qa/qa1623/_index.html
It is not possible to remove support for existing devices. The only way is to create a new iPhone-only app.