What does it mean, on a molecular level, to "touch" things? It's just repulsion of electrons. So if Harry has learnt to do partial transfiguration by considering things to be just piles of atoms, he might also be able to get around that restraint.

Of course, you are still completely right that transfiguring stuff into very small particles is quite dangerous: What if the atom sublimates? What if somebody somehow takes it up so it becomes part of that person's body? How to find it in case it gets lost in the atmosphere, in the sea, or anywhere else? Etcetera. All sorts of fatal mistakes can be done, and Harry will not want to risk dying, or making Hermione's recovery impossible.