Is this supposed to be funny?

Yesterday I went to a Catholic mass for a First Communion ceremony.  Everything was fine until the very end of the mass, when the priest told a joke:

A United States Marine was attending some college courses between assignments. He had completed missions in Iraq and Afghanistan.  One of the courses had a professor who was an avowed atheist, and a member of the ACLU.
One day the professor shocked the class when he came in.  He looked to the ceiling and flatly stated, 'GOD if you are real then I want you to knock me off this platform. I'll give you exactly 15 minutes.' The lecture room fell silent. You could hear a pin drop.  Ten minutes went by and the professor proclaimed, 'Here I am  GOD, I'm still waiting.'
It got down to the last couple of minutes when the Marine got out of his chair, went up to the professor, and cold-cocked him; knocking him off the platform. The professor was out cold. The Marine went back to his seat and sat there, silently.
The other students were shocked and stunned, and sat there looking on in silence. The professor eventually came to, noticeably shaken, looked at the Marine and asked, 'What in the world is the matter with you? Why did you do that?'  The Marine calmly replied, 'GOD was too busy today protecting America 's soldiers who are protecting your right to say stupid stuff and act like an idiot. So He sent me.'
The classroom erupted in cheers!

The whole congretation laughed.  This was interesting to me and I had a number of different reactions.  The first reaction was from the gut (OMG not all atheists are arrogant and pompous and use their classrooms as a soapbox!).  Then I thought wait a minute, why are they all laughing and I'm not?  I wasn't offended by the joke.  I'm used to that characterization of atheists AND I was on their turf. The difference in our reaction to the joke is what interested me.  I think that they saw the joke as "good Christian boy stands up for God/his beliefs, and is witty to boot!  Haha!", whereas I saw the joke as "young man creates violence in the name of God/religion, and the rest of the class applauds him".  The fact that punching someone in the face so hard that they are out cold turns from "bad" to "good" when said person is an atheist (AND a member of the ACLU!  For shame!) is sad, and honestly a bit frightening.