Fitrah of a humam is what defines the human according to how he is built to function. Part of the fitrah is an a-priori knowledge of the good and the evil. When one intends to do any evil, an inner voice of conscience warns him against it. Using his free will, a human may ignore his conscience and still commit the evil. If he continues to do this consistently, his voice of conscience keeps getting weaker – sometimes to a point where it stops working altogether.
What you’re referring to as silencing the fitrah is in fact silencing your voice of conscience. When your conscience doesn’t function as it’s supposed to, you’re prone to committing more evil and eventually pay the price for it sometimes in this world as well, but definitely in the hereafter.