The fact of the matter isn't that the negatives are just a little dirty. They have deteriorated as film does. The point will come when no amount of work can be done to lift usable images off them. It's the same kind of thing with LaserDiscs, rot and warping. Let's say you have a rotted, warped LD. What are you going to do with it? You'll want to lift the images off it into digital preservation as soon as possible, so that it doesn't deteriorate any further. So you get the best player you can, tap the video stream early on, before any comb filters are applied. You then do what you can to de-warp the disc, and make it flat again. And then you clean the disc so that the areas effected by rot will be read as best as possible.
In two months your LD looks exactly like it did before you cleaned it for your archive project.... That's why they wanted to continue to clean the negatives. They may never again have the opportunity to digitise the SW negatives to the same quality that could have been achieved then.