Actually, it's perfectly possible to embed fonts in iBooks. I documented the basic technique in
a blog post.
Essentially you can use any font, but it must be converted into SVG font format. Also, although it is possible to replace the entire text with the embedded font, it is extremely slow and carries other drawbacks. Still, for rendering individual characters, such as for math or isolated non-Latin words, this method works quite well.
However, for your situation all you really need is accented Latin characters, which I'm pretty sure the iPad is equipped to handle. I haven't done this before. But here's a guess: save your file using UTF-8 encoding. (It should be in UTF-8 anyway. Make sure your headers specify UTF-8 as well.) Then just use the actual character instead of the HTML-code.
Let us know how it goes!