Maybe this is a partial answer to Raven's concern that he's sounding paranoid.
Without denying that a base commander has the right to control his installation, and recognizing that the USAF in particular has had issues with aggressive proselytizing, I still don't understand how this happened. This was a retirement ceremony, so even if he was the most annoying Jehovah's Witness in your command you'd think you'd let him have his party and then just go away forever.
I'm also not sure why the base commander would forbid the use of the word "God" in a retirement ceremony anyway, any more than at a wedding ceremony conducted on base.
Besides, the speech is nondenominational, just the ordinary linking of religion to boilerplate patriotism. "God bless our flag, God bless our troops, God bless America" is not exactly a call to join some particular church.
It'll be interesting to see how the Air Force explains just what happened here.