So perhaps ... one highlights a region containing a hole, the surface around the hole perimeter (perhaps excluding the "bleeding edge" itself, for quality reasons) defines an average plane orientation and position, the hole gets filled in automatically, using facets of a similar density to that of the surrounding mesh, you then select a different region of surface, the software calculates the relative average plane and angular and positional offsets of that second surface, and then as you move the mouse with a mouse button pressed, the software influences the heights above and below the initial target mesh by the heights of points above and below the local average of the second mesh region. Successive strokes make the influencing effect stronger, up to 100% ... or just use a paint strength of 100% by default.
Also, don't limit the the surface painting to the perimeter of the filled hole, also allow overpainting the surrounding region.
Actually, this could be a nice feature even for regions without holes, or where holes have already been filled. Might work nicely in conjunction with a "subdivide mesh" brush, so that one could take a low-res section of mesh, subdivide it, and then "paint" the positions of the new "uninteresting" points with the surface from a more interesting region.
Hm. I wonder whether Blender or Meshlab have a function for this?