May be easier to use a DNA dye that penetrates lipid membranes (although I do not know if they pass thru a cell wall). You may have to add a permeabilizing step to punch thru the cell wall first. Since cell walls are high in polysaccharides, maybe some enzymes directed there can expose the plasma membrane.

Cleanest way is to purify the nuclei, but that is a bit of work, one aticle below:

http://www.researchgate.net/publication/249963574_AN_OPTIMIZED_METHOD_FOR_THE_ISOLATION_OF_NUCLEI_FROM_CHLAMYDOMONAS_REINHARDTII_(CHLOROPHYCEAE)_1/links/0c96051e74e0a56f3e000000

Data AN OPTIMIZED METHOD FOR THE ISOLATION OF NUCLEI FROM CHLAMYD...