SpaceX usually deorbits their second stage rockets over the ocean in a controlled manner. The article you linked is about a one-off case where the rocket engine

SpaceX usually deorbits their second stage rockets over the ocean in a controlled manner. The article you linked is about a one-off case where the rocket engine failed to re-light and ended up reentering in an uncontrolled manner. There's a big difference between something like this happening due to an accident, and it being done on purpose as a matter of course.