Heh. Careful what I wish for, eh? I have to say that while I do see this fic as dark and I don't think it can possibly end well, that I'm not quite sure my heart can take a truly unhappy ending for two such lonely characters. *I* was afraid of Harry, but I'm not sure I really want Snape to be afraid of him.
That said, I do see Harry as a loose cannon and I don't imagine he would stop at anything to keep Severus with him. A confrontation with Bill would be inevitable. Snape would have to have some reason for no longer wanting to see him and the truth seems like a dodgy option. And, really, it would probably be safer for their 'cover' if he were to continue seeing Bill until it could end naturally with Bill's marriage. I can only imagine what Harry would make of that.
And I think it would only be a matter of time before Severus was asked to leave his position. I doubt very much Harry would take that well. Not sure how I feel about Harry picking off Weasleys as a message to Snape. I don't think Snape is all that close to them. Though I can imagine Harry trying to spend more time with them so he has an excuse to be closer to Snape and I can see him using Ginny to make Snape jealous.