As I said below, perhaps the specified fonts should be a default with alternatives in a menu, but until then, it's vastly preferable that they use the reader's font and not the book's.
This isn't a printed book, as the woeful justification should prove. Designers don't get nearly as much control.
(Ultimately, I think they will offer an option to use the specified fonts. There's so much wrong with iBooks it feels like the most unfinished 1.0 product out of Apple since Aperture)
As for putting them in the browser: a vanilla browser is possibly the worst way to display seriously large amounts of plain text. By the time you've added all the custom elements needed for good reading, you're at a full app anyway. It could be a web app, sure, but that's a different discussion.