It sounds like what you want is to do is make a Marker invisible based on some data about the marker. My recommendation:
-Subclass the MarkerControl class
-Add 2 Visual States (Visible/Invisible)
-Inside your MarkerControl class switch to the Invisible visual state based on the Marker it is bound to
-In Blend make your MarkerControl class invisible when the VisualState is Invisible
-Change the DataTemplate of the MarkersElement (inside the Scrubber template) to instantiate your custom MarkerControl class instead of MarkerControl
I think that ought to do it but let me know if you have any trouble.