I would also like that. Right now it's too transparent, I always get USD and have no idea whether someone paid with Bitcoin. I'd like to just keep the Bitcoin.
Our users tend to want unified behavior across payments of all different types. Of course, it's possible to filter by payment type in the API, dashboard, and data exports.
To the original question: drop us a line at bitcoin@stripe.com if you want to talk more about not converting the payments. It's definitely something we'll support if there's user interest, but it's not something we do today.