I don't think I've ever read a story where someone actually *uses* a safe word, and it's interesting to me that it's more emotional intensity than physical discomfort that triggers Harry to use it. The aftermath is also quite compelling, the instant and absolute way that 'Silence' ends the scene and moves to reassurance and comfort. Of course, I've only the spottiest, entirely theoretical and third-hand (i.e. garnered by reading fic and the occasional non-fictional discussion) of BDSM, and it doesn't particularly appeal to me, so probably my surprise is just an expression of my ignorance. :) Anyway, while I personally don't see the attraction is most of the kinks you explore here, you do an excellent job of conveying how intensely Harry *does*, for which muchos kudos.
I enjoyed your working in of other canon characters, and I loved the conversation between Harry and Snape, with Snape all up on his 'do you know who I am, you dunderhead' high horse, and Harry, so different from his 'Seeker' self, very forceful and just plain not taking any of Snape's crap. And the idea of the scene where they discover each other's 'real identities' just makes me laugh.