It may seem silly, Banjer, but as I understand it they were following the stated rules of the show, which prohibited religious songs. "Kumbaya" is a religious song, the title being a phonetic rendering of "come by here" as spoken in some African (I think) accent. The song essentially says "We're singing, praying, etc., Lord, so come into our midst."
I would presume they prohibited religious songs so as to avoid offending people's sensibilities, which some of the more strident religious songs could do. Now, "Kumbaya" is about as mild as religious songs get, but if you make rules, it behooves you to stick to them. Unfortunately, that doesn't guarantee that no one will get offended--in this case, some were peeved that the song was disallowed.