I did exactly that last week.
Go to the DefaultInitializationErrorHandler component.
Comment the OnGUI() method to get rid of that white and green screen (Vuforia should really create a proper prefab instead of using the GUI..). Take a look at the method SetErrorCode as you may want to re-use the mErrorText message from your own popup. You could also directly customize that class as you wish, beware if you update vuforia in the future :)
Please note that I am using Vuforia's DelayedInitialization mode.
In your game init class, right before you call VuforiaRuntime.Instance.InitVuforia(), type: VuforiaRuntime.Instance.RegisterVuforiaInitErrorCallback(OnVuforiaInitializationError);