Luther's break from the Roman Catholic Church after the posting of his Ninety-Five Theses in which he objected to the selling of indulgences, for instance, gave rise to purification in religious sects such as the Anabaptists who sought to rid Christianity of all the "frills" of architecture, sculpture, doctrine, etc. For one thing, rather than a hierarchy, churches began to have a more lateral structures.
Certainly negative effects came of the Protestant Reformation as England engaged in a religious civil war, and France expelled the Huguenots, members of the Reformed Church of France influenced greatly by the writings of John Calvin. These Huguenots moved to other Protestant countries such as England, Denmark, Switzerland, and the Dutch Republic. While Christianity was not in decline, it certainly had much dissension and death connected to it.