It’s entirely possible that this is entirely natural. Hermione beat Draco badly enough to put him in the Hospital Wing; either he’s legitimately near-death, or Lucius blew it out of proportion.
Alternatively, Hermione and Draco actually talked it out and are currently laying a mutual trap to figure out who’s using them both as pawns. I like this option, but it’s also probably the least likely one.
Personally, I’m worried about how Harry will react. He’s not going to take this well, certainly.
Now, the question here is how intelligent Hermione was. If she left the letter somewhere Harry can find it—or would know to look—then Harry would at least know what happened. Probably couldn’t be used as evidence, but it would help.