Perhaps I'm just overly simple here, but it seems to me that Draco decided to do the murder setup when he was writing the letter. I understand that it could be a lot more complex than that - but not everything -has- to be complex.

My prediction: Draco dueled with intent to frame Hermione for attempted murder. Hermione sat next to HP because she knows she's screwed and there's nothing she can do about it, and she wanted to be near him when the inevitable caught up to her.

This prediction creates what I'd consider an extremely messy political problem for HP, one that quite frankly I don't see an easy magical or non-magical solution to. That may be the point.