It's not just Hagrid. Most of the main characters in the US editions have individual fonts for at least their signatures, if not whole notes/letters, as do advertisements, proclamations, etc., but as I've said
before, I highly suspect we are in the minority there. The rest of the world got on with the story just fine without having a dozen different fonts, so it's not like that part of the formatting absolutely must be preserved at all costs (assuming mobi really can't replicate it, and I don't have enough format know-how to say for sure it can't). For that matter,
most of the books I rebought electronically don't have the same fonts/formatting as their paper counterparts, even with publisher defaults left on, so I don't see why the
Harry Potter books have to. I like the extra fonts, sure, because they add a lot of flavor to the story, but they're not an absolute necessity. And, frankly, I'd have sacrificed them to keep the text from the Bloomsbury editions, but that's a whole different soapbox.
All that said, I'm skeptical that Pottermore is going to force Amazon to support epub or any other similar such standardization. We already know the books are going to be DRM free, so the files just need to be multi-format like Smashwords et al. Especially since the original press release/FAQ said they were going to try and offer as many formats as possible. There was nothing about that which suggested format standardization to me. *shrug*