Although the pigment inks are water based, once they are dry, they are water-fast. Kind of like the water based latex paints in that regard. So you might have lot more choices than you think. Never done any painting on an inkjet print, but have dabbled with doing Pt/Pd on top of a pigment print which withstood all the wet processing fine. The dye based inkjet inks on the other hand are water-soluble after drying so they won't work with water colors, but presumably you could use a proper solvent based paint for it.
Good luck...
:Niranjan.