Hit points are more than just a nod to old-school D&D, but yes, that heritage is the only reason they're in the game. The Harm Clock would have worked equally well from a mechanical point of view. It just wouldn't have had the right "feel". For darker fantasy the Harm Clock would be very well-suited.
Dungeon World was made to play D&D-style adventures without the fuss that the authors personally found disagreeable, but still retaining the feel and style of D&D at its best. Hit points made the cut.
One notable difference to watch out for between Apocalypse World and Dungeon World is how combat is a fixed three-round affair in the first and a fluid part of the ongoing fiction-move flow in the second. The fixed-round combat is tuned so that it works well with the Harm Clock; the fluid combat system tends to be much more variable, and suits the small gradiations available with hit points. Neither are strictly incompatible with the other, but you should keep in mind that each injury subsystem developed in the context of their own combat assumptions (or the other way around), so when switching things up, look especially hard there for unexpected interactions during play testing.
My only source for this is observations and conversations during DW's development about sacred cows, Adam's particular frustrations with their AD&D game, and Tony's Apocalypse D&D hack that started it all. For what it's worth.