The fallout also settles in the streets--and that means nobody leaves those buildings for almost a week. Also remember that the localized EMP will clobber the local power grid--no refrigeration. The ground shock fractures the water pipes--no firefighting capability, plus no drinking water. Most of the buildings in the lethal area will not have window glass, so external air will circulate into the buildings.
Blow the thing off at lunchtime, and you've got a million-plus people out in the open for the crud to land on.
People would be able to travel in the streets to be evacuated. You can survive heavy radiation doses for a short time. I remember talking to a friend who photographed inside a nuclear reactor after an accident in the fifties. He said the film was so badly fogged by radiation that they had to go back in and re-shoot it.
A ground burst would not cause nearly the fire damage that an air burst would because the most of the city would be shadowed by the nearest buildings.
Lack of water, electricity and refrigeration are pretty much standard inconveniences that we deal with during disasters.