I'm kinda assuming that the entity Collette discovered is in fact the MoP, what with her observation that its focus is shifting being immediately followed by her father scolding her.

On the way he deals with people Sparks that learn too much about his secrets, well he has to do something.
Making very clear that poking certain aspects of his city will lead to... unfortunate consequences is most likely slightly more effective than telling them not to.

Besides, he is still a Spark.
Somewhat over the top reactions are to be expected.

More importantly, Tarvek, Gil and the Clank-guy kinda prove you can avoid the consequences if you are clever and quick enough.
So I guess it is more like natural selection for mad scientists than a punishment.