I know the concern. I had a leak from the upstairs neighbors' bathtub that came through the ceiling near the rat cage. While the workman sanded and repainted, I moved the rats into a temporary cage in the bathroom (my apartment is a studio) and covered the DCN with a tarp. I also tried to vacuum up as much plaster dust as possible before uncovering the cage and returning the rats. It seemed to work; I never noticed any problems.
Another suggestion besides those already posted is that you could tape a sheet of plastic over the rat-room door to help keep out dust. It won't be perfect (construction dust can get through everything), but it will help a lot. The real risk, to my mind, is not so much dust and the like is the volatile aromatic compounds from solvents and paint. I suspect, however, that since the work is downstairs and the rats are upstairs, they will probably be fine. Still, if you're really concerned by the strength of the odor, take them out for a few hours during the repainting (keeping the rat room shut up, naturally) and they'll be safe from the worst of it.