When Benjamin interrupts the wedding at the end, it's the high point of the movie. Mike Nichols and Buck Henry discussed how he wanted Benjamin to appear to be sealed in, cut off from the outside world—as he is in the scuba-diving scene—and the image of him pounding on the glass church window on the second floor is meant to give that impression as well.
As the wedding guests try to stop Elaine and Benjamin, Ben fights them off with a large cross, which he then uses to bar them from leaving the church. He's "seized the sword" at this point, heroically (or anti-heroically) affirming his destiny, locking everyone else into the world of "plastics" while he and Elaine go off to seize their destiny. The church wedding represents the traditional expectations that Ben and Elaine are upending.