You kill the other larvae so that the bees pick the remaining larvae for queens. That way you can control the location of the queen cells on the frames. If you don't kill the others, then the bees may or may not use the larvae that you wan them to.
I read a similar idea in a little pamphlet in my local library. The guy would use bullets, I don't remember the caliber, to cover up the larvae that he wanted to be queens, and then would powder the rest and kill them. He actually spelled out words on a frame and the bees drew out queen cells in the shapes of the words. This way, if I recall correctly, didn't break any of the bottoms of the cells, the bees take care of that.