She says that outright though, doesn't she? "What if he's done it to us with all of his cases?" or something along those lines.
That's her, it's who she is as a character.
She's the first person in the first episode to doubt Sherlock and she's the most eager for her suspicions, her beliefs which she's held for years, to be proven right.
The basis of her sudden suspicion is, after all, that nobody could do what Sherlock has done in every single one of those, so if he could've done it in some of them, there wouldn't be a basis for that.
It's not a sudden suspicion though is it?
Ultimately, it's in the execution, and that wasn't the least bit convincing. Not the sudden way in which they turned on him, not in the way Lestrade fell in line, not in the way the superior was acting, not in the way Sherlock himself reacted in running away, not in the way nobody bothered to find out why the girl reacted the way she did and so on. And there were a lot more things like that in that episode. I'm afraid talking it out won't help, either, I just didn't find it a lot more convincing where that aspect of the plot was concerned than you did with Hound of Baskerville. I did like it better because a lot of other stuff was very well done, I liked Moriarty a lot in general and the first half was fine where all of Holmes' interaction and dialogue was concerned, and the Key idea in itself and the way Moriarty starts it off, I can buy. I just wish the whole framing Sherlock thing worked better.
And as I've said, I agree with you on some of it, it wasn't perfect.
But I think you're taking an extreme position yourself and ignoring some of the evidence that's was in the show. There are flaws there, but other bits I just don't think are the way you're presenting them here.