It actually doesn't much matter who the "she" is. And no, I didn't imagine it was Ginny. Just... someone who came between them. Not even romantically, just someone who made their relationship strained. Who caused problems for them that they couldn't- or weren't willing to properly- resolve.
And, yes. Severus is definitely thinking. Trying to figure out where he went wrong, and what- if anything- he can possibly do to fix it. And that's hard for him. And he's beyond unable to understand how Harry could have just walked out on him.