Aren't you supposed to leave some clues that point in the wrong direction in a frame job? As far as I can see, there is really no evidence implicating Marienburg, and a little bit for the Empire or the Skaven. But that evidence was very hard to find and relied on investigation by skilled mages, which is not something the attackers could have counted on.
For a frame job the whole thing just seems to mysterious.
Current events and tensions have made it so that anything targeting shipping on the Skull River is automatically attributable to Marienburg unless proven otherwise, because that's one of the two supply pipelines for the canal construction.