You are never really going to get ideal results cutting holes (trimming) and then trying to convert back to poly's.

The best workflow would be to use the advantages you get from the nurbs to create the object including the holes and then retopologize by drawing polygons with the correct topology using the nurbs surfaces as a guide (you can make them live).

You can also make them very dense, then convert them to polygons, then export them to a retopo package to do the retopology.