Haa, I rode this late at night when MK was about to close last week.. and the skipper went off script as well. I didn't hear any of the chanting though, now I know to listen more closely when we go back.
I also don't mind them going off script, I found it really entertaining.
Start the video at around 5:02 for the full explanation and at 5:24 for the actual line... but (at least in this video) it is explained (by the cast member giving the tour) that they are actually saying "I love Dis. Co." (as in an abbreviation "Disney Company")