You can leave the end mill in and tell MeshCAM to only finish areas that are less than some shallow angle- maybe 20 degrees. You could then do another toolpath with only waterline finishing using the ball mill and tell MeshCAM to only machine areas steeper than 15 degrees. (The overlap makes sue that all areas are machined without gaps).
This method would give you a pretty good finish with the right cutter for each region.
-Robert
(Note: The opinions expressed in this post are my own and are not necessarily those of CNCzone and its management)