This is an instance of the idiom "Now you've done it!" The basic meaning behind it is that someone has done something bad which is the final straw/will get them in trouble for whatever reason. I don't remember exactly what happened at this point in Harry Potter, but the idea is that whatever Harry did to get McGonagall mad at him was very bad, she is extremely upset, and it's likely he's going to get expelled.
A couple other examples of this phrase's use:
John breaks a lamp.
Mary: Oh, now you've done it! You're going to be grounded for the rest of your life!
Or perhaps:
John pushes the big red button, loud sirens start going off.
Mary: Now you've done it! We're all going to die here, aren't we?
