Don't get me wrong, I'm almost always on the side of: "It's the Defense's job to stop them" argument, BUT, this is a service academy. I don't like seeing a team run the score up on a Navy, Army, or Air Force team.
Notre Dame had 43 points, so they punched one more in at the end because 50 is a nice round number. With :39 seconds left --- take a knee when you're playing against kids in the service academy. With :39 seconds left --- it's the norm to take the knee.
I think it's a classless move by Brian Kelly, but I'm not surprised.