I don't know what problem people have with your story, here. I had tears in my eyes because I could almost feel Harry's hurt when Hermione tossed him out like that without even hearing him out.
I understand that it hurts to discover your significant other "might" have cheated on you, but in all fairness, what might be probably isn't. Hermione--ever so logical--didn't bother to keep that in perspective.
I don't blame Harry for leaving, especially when people who professed to love him dragged his name through the mud over something that was none of their business in the first place. I've had people turn on me and it's like being shot with arrows right through the heart. Harry has trust issues as it is, and this just shattered any trust he had for the people in his life. They've got a long road ahead of them if they think they're going to regain it, because Harry doesn't trust very easily or very often.
Ron and Hermione--Harry's best friends. At least they're harboring some guilt for their stupidity. I just hope it isn't too late now.
Mechanically, you have a couple of errors, but nothing horrible. They need to be addressed, but they're not detracting from the story at all. You're doing fine.
And as for people telling you how to write your story or who to pair who up with, forget that. This is YOUR story, so you write it however you want to. GOOD JOB!
Author's response
Thanks a lot for your helpful comments. I'm glad I'm getting across some of the pain and anguish that people are supposed to feel after such a detraction of trust.
As for the mechanical errors, I know they're there. Sorry for that. The thing is that I catch some of them not all though. And I wanted to get this story down before the idea completely dries up.
I'll update soon, I have three chapters ready and waiting just waiting for some polish. Thanks for reading, hope you continue to leave comments!