I see a couple threads on this, but none really speak to what I would like to do. I am trying to write an application that will deny another application the ability to conn
Build Perspective
Even with a rooted phone, because this is handled by the frameworks, I highly doubt that you can achieve something like this.
Specifically unless you have the source and can compile the source of a new phone, you cannot do this.
SDK Perspective
Also another thing about this is you can't "strip" an application of its permissions BECAUSE its in the Manifest.xml which gets embedded into the .apk of an application, which is a binary and is registered with the PackageManager.
This is far beyond the scope of the SDK.
What you CAN do is kill an application if it isn't to your liking. The PackageManager would be your best option, however; that is as far as you can go.
Update
Check this out: http://android.amberfog.com/?p=98