I haven't done a careful reading of HBP, so I try not to rely on my memory about it, but that's the way I remember it in HBP too, that Harry just assumed a reasonable scenario for Dumbledore accepting Snape back into the fold.

I'm actually not sure why anyone would want to believe Harry's conclusion, since it's so mundane. Surely it would be more interesting if it were something more complex and specific than "spinning a tale of deep remorse". I know that's what I'm expecting.