Apple has introduced the possibility of deleting an app. Quoting the iTunes Connect guide:
If you have created an app in iTunes Connect that you no
Follow Below Steps
Login into your iTunes Connect with your developer id: https://itunesconnect.apple.com
Click on App Icon
Click on Rights And Pricing
At the bottom This app will be on sale in all App Stores worldwide. Or, you can select specific stores “here”. Click on here button to open all specific app stores.
Click on the “Deselect All” button to uncheck all App Store territories.
Click on “Save Changes” button.
Now when you save all these and go to back to your App icon home screen. There will be one more button appear “Delete Application” after “Set Up iAd Network”.
Click on Delete button and read instructions.
Your app will disappear from the app store within 24 hours.