Well, next chapter will help clear up some of this, because Hermione and Harry will have a talk.  What has been established so far is that Dumbledore asked Hermione to stop hanging out with Harry, and being the "adults are always right" person that she is, Hermione's first reaction was to do as she was told.  She's beginning to regret her actions, though, as shown by the comment that she coudn't bare to lose both her friends like that.  She didn't go down there to rescue Harry and Severus.  She was headed to class and happened to find them.

So Harry and Hermione will talk next chapter, cry a little, make up, she'll apologize, and Harry will forgive her.  They might be able to figure a few things out about Ron as well.  I think the problem that's presenting itself in this story is that I'm writing almost exclusively from Harry and/or Severus' POV.  And since they're probably the two most out-of-the-loop people, it leaves the reader a bit more in the dark than if I chose to write from others' PsOV.  For example, please notice (it's a clue) that I have never written from Dumbledore's POV.