Note that he does not claim that they are not real and that those who experience them are lunatics or liars. For to do that would be to condemn Rav Yosef Karo and Rav Moshe Chaim Luzzatto.
Rather, he claims that they are certainly real. And there is no "sour grapes" here, where he is condemning something because he himself does not merit it. Rather, many maggidim wanted to teach him Torah, and one even implored him greatly. But he rejected it. And he instructed his student (Rav Shlomo Zalman) to ignore the overtures of a maggid as well.
Thus, none of his own Torah may be attributed to maggidim. And he claims that his own Torah is better, as it is not through an intermediary. And maggidim might be serving the sitra achara, and thus misleading.
But will he slight Rav Yosef Karo? No, he answers (in instruction Rav Shlomo Zalman) with an apologetic of nishtaneh hateva! Of course Rav Karo's maggid was entirely holy, with no sitra achara. But that was in Eretz Yisrael and when the generation was fit. But we, with yeridas hadoros, and living outside Eretz Yisrael -- of course we should avoid maggidim, because it is impossible that there would not be some admixture of the sitra achara.
Does this not seem very much like an excuse? If I knew that my kabbalistic followers were not ready to dismiss this superstitious, and if I did not want to insult those who had used maggidim in the past, I would come up with such an explanation which insults no one but still entirely deflates the practice going forward in the future. "It was OK for them, but not for us." Does that line sound familiar?
Of course, it also is possible that he meant exactly what he said. But of course, I do not believe that dybbuks are anything but psychotic episodes, and that maggidim are hallucinations or fictions. So I don't see how the Gra could have discussed this with them. (Of course, mystics would have no issue with this.)