since no one is answering this question, I am going to answer myself. Based on current research, there is no way to do this at iOS 6. However at the iOS 7, there seems a new feature added to manage open in per these 2 links although I haven't got chance to look into API yet.
- http://www.pcmag.com/article2/0,2817,2424581,00.asp (open in management)
- http://www.maas360.com/products/mobile-device-management/apple-ios/ (Manage open in)