The Medal of Honor is rarely awarded to someone whose bravery didn't cost them their life. In this case, it cost the soldier a limb. He deserves the honor and recognition of the award, but I don't see why they needed to begin the ceremony with a prayer (video). It's followed by a presidential speech. Why not start with a generic speech by a general, and then the president could bring up all the points the chaplain worked into his prayer, without the rhetoric of "God" blessing the nation and making us special blah blah blah
The chaplain starts by crediting God but then segues to the guy's honor and courage, then goes back to asking God for blessings again. At the end, he quotes Calvin Coolidge (not a Biblical "author"): "A nation that forgets defenders itself will be forgotten..." and then follows with a very Christian ending "in thy holy name, Amen."
The man's colleagues were saved by his bravery and quick thinking, not by prayer or a higher power, or else they'd be awarding the Medal of Honor to Zombie Jebus instead. They were honoring a PERSON and they didn't need to sully his accomplishment by referencing an invisible sky daddy, even if they believed there was a sky daddy behind it.
It cheapens the award to make him share the credit with a God, and it denigrates other soldiers to call upon God for continued safety instead of the bravery of the soldiers themselves. If that's not reason enough to eliminate prayer during government ceremonies, I don't know what is.