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SUCCESS!!! Patched app passed the validation!
Just checked the build with and without the validation - GameKit is still there.
Checked build with new Unity 4.5.4 - GameKit is still there.
I have made a script, that applies the patch to the build. Works out of the box on Unity Pro - just add to the project and it will remove GameKit...
The same problem. Unity, please add the ability to remove GameKit from the build.