The footprints of the towers are the two 280 ft. squares where the Towers used to be located.
The footprints (and the entire sixteen acres, depending on who you talk to) are considered both "cemeteries" and sacred ground by some even though the site has been dug out down to the original concrete foundation and there is now nothing at all buried there, let alone any "ground" (there never was any earth at all down there after the WTC was built, aside from a few planter pots). I have no problem with devoting the footprints on the surface to a memorial space, but I have to wonder about the people who feel outrage at the thought of the subway being restored along its original lines, as if there was anything down there to disturb right now except air.
Filling the two squares with seven stories' worth of dirt and planting trees will not ever turn the site into a cemetary, no matter matter what mental and emotional gymnastics accompany the process. The subway tunnels should be restored in the swiftest, most economical and PRACTICAL manner available, without having to divert them around merely to pander to the illusions of a small group. The tunnels will not affect what is built or not built on the surface.