Of course, we know that dybbuks don't exist. Just as there is no demonic possession which an exorcism by a competent priest can remove. The evil spirit which entered the man in Vilna was just the man having some sort of psychotic breakdown. I think, with my limited knowledge of the Gra's positions, that a plausible theory is that this is a way of opposing without forcefully opposing, directing himself and his followers not to tread these paths (such as maggidim), not because they were false and the people engaged in them were superstitious (even though that was the truth), but because it is possible that could come from the sitra achara and mislead people.
Whether or not the Gra believed this, is seems a "useful" approach.