There will be an explanation forthcoming for how Daphne took down the wards in the next chapter (or maybe Chapter 18, depending on how long the fight with Cordelia lasts).

Harry has kind of accepted his emotions because he has no choice. Once things calm down- especially given what happens at the climax of the story- he may have other ideas.

Harry is powerful, that's true, but recall how much he can't trust his magic right now. He may want to save Draco, it may do something extreme, he'll panic and try to restrain it, and Daphne will have a chance to strike.

Harry might try to change his priorities by sheer force of will.

And yes, the potion would affect Harry's magic only when it comes to Draco.

Thanks!