Lightroom 4: fixing skies

+1 for blue luminance under HSL.  Reducing it will bring back blues from the sky.  It's the lowest effort/most real looking result I think that you can get, but it's not dramatic.

As for brushing, you can do the ND filter and then brush back anything that pokes up into the sky.  I think that's invesrse of what was described and seems quicker to me.