Update: be aware as this is not working on iOS7, however in iOS7 MapKit officially supports to disable base layer !

This blog : http://blog.sumbera.com/2011/09/18/how-to-disable-base-google-maps-in-mapkit/ wrote about how to disable Google maps in MapKit. Now with new iOS6 and brand new Apple maps and OpenGL rendering , the question is how to disable rendering of the base maps without using undocumented functions. Removing whole base layer (VKMapView) is possible but cripples touch handling of the overlays. So here is very simple way how to do this without removing VKMapView – just set opacity of the layer to 0.0. This will erase base iOS6 maps .

+(void) eraseiOS6maps:(UIView*) mapView{
   // -- get rendering layer
    UIView *rootView = [mapView.subviews objectAtIndex:0];
    UIView *vkmapView = [rootView.subviews objectAtIndex:0];
    UIView *vkmapCanvas = [vkmapView.subviews objectAtIndex:0];
   // -- set opacity to 0.0 
    [vkmapCanvas.layer setOpacity:0.0];
}

View hierarchy:

MkMapView/UIView/VKMapView/VKMapCanvas
MkMapView/UIView/MkScrollContainerView/MkOverlayContainerView/MkOverlayClusterView/<your overlay>
MkMapView/UIView/MkAnnotation/...
MkMapView/MkAttributionLabel