Beetle was already on the way down, because he was holding a Hive engine against the direct orders of the Baron. It is true that he was also sheltering Agatha, but the two facts don't seem to be related (there may have been evidence in his notes, but Doctor Merlot burned them).
Stumhalten's fall is largely down on Anevka and Tarvek. Anevka assasinated her father, and the cover-up attempt raised a big red flag to the Baron.
The Baron takes himself out of the picture because he had been wasped by Agatha/Lucrezia and is being influenced by Anevka/Lucreczia. Again, Agatha has been around for a long time before the Baran went down, and Agatha/Lucrezia is down to the Geisters (Tarvek's father narrowly missing responsibility due to being dead).
In the background Zola, as the Queen of the Dawn has slowly been taking over large sections of Europa. Agatha is not involved in any of those kingdoms falling.
The Master of Paris was brought down by the Other or by Zola (it isn't stated which, but the smart money is on Zola). The rebellion in Paris was organised by the Geisters, and had clearly been setting up for a long time. Far from being a cause, it is Agatha's presence that disrupts it.
Related to the rebellion - The leader of the Library was assasinated by Tarvek's family; Laurana's dad was already in with the rebellion in Paris, and was taken out by Laurana. True, Agatha was there, but Laurana's motivation was saving Jim Hoffman, and I think she would have acted the same way, Agatha or no.
Martellus was already in charge of the family before the time slip. When he goes through the time-slip he has to get it back again (which he seems to do very quickly).
Edit: And I forgot about the Corbetitites. Thanks, Geoduck.