That's the annoying thing. Hollywood thinks their audience is stupid. Maybe they are only projecting and they themselves are stupid.
The irony is that, since Khan was a secret, people went to see Cumberbatch as John Harrison. Yes, they actually wanted to see an original villain, because you advertised the film that way, you fools! There was absolutely no financial benefit in having Khan in this.
I'd tend to agree with your first sentence except your your bottom paragraph basically proves them right.
Anyone who seriously thought that John Harrison was just going to be John Harrison was an idiot. From the first time I hear of the the serious inclusion of the Botonay Bay post credits scene that they were going with Khan in the second movie.
Not only did it only make the most sense in the world, all of their rumored casting choices gave it away, even when they went with a less obvious choice, everything was pointing to Khan. If nobody figured it out by the time the first teaser came well before the actual film, and they still thought it wasn't going to be Khan then they deserved to be let down.
Seriously, it was a very poorly kept secret. Most people just seemed to be in some kind of denial about it.