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TrE comments on Harry Potter and the Methods of Rationality discussion thread, part 23, chapter 94 - Less Wrong
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Or transfiguring the body into something that doesn't change very much over time even if it is warm, such as an electron or a molecule of nitrogen and store that safely (what about a single carbon atom within a diamond? Should go about unchanged, and is easy to store).
Actually ,there's an even bigger problem. In order to maintain the transfiguration, you'd have to touch that carbon atom again.
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.
I'm not sure you can transfigure things into individual atoms, though. It's been implied that large scale changes are hard, and the scale change from body -> gem is, what, twenty orders of magnitude smaller than that from gem->atom?
Now, the real ideal would be some supercooled perfect crystal of nitrogen or something. But that has... obvious problems.