You make an interesting point here. But I think this might actually work out even if it comes to light to Severus what happened. With time and distance Harry might be able to gain confidence in Severus feelings for him and if it ever comes up again he might be able to say that it was a stupid mistake borne of a lack of comunication, or at least, Harry's inability to understand. And the fact that Harry won't have felt the need to stray anymore might help his case.
As you can see I'm hoping for a sequel. XD