Hitwise rely on purchasing data from ISPs, which will also run into a couple of difficulties along the way.
Personally I don't see why doubleclick or atlas can't make some kind of tracking system. They should be able to give decent estimates as to the size of each site from the number of adverts they serve to the sites. They will definitely be able to estimate the crossover with other sites.
There would be the usual privacy concerns, but I think the data will be collected in a reasonable way. We'll see what happens.