You also have to take into consideration that SOTS was the highest-grossing movie of 1946. The second was Notorious. Even if it was a financial failure, none of the movies released that year did very well. The economic boom hadn't happened yet. All of the music in both movies and musicals were all excessively happy or positive--about bright and beautiful days, because WWII had just ended and we had just m*rdered a bunch of Japanese civilians. So whilst Zip-a-dee-doo-dah might also have problematic origins, it falls into the same pattern that every other song of that time period. Musicals like OKLAHOMA!, CAROUSEL, ALLEGRO, STATE FAIR, ON THE TOWN, BRIGADOON,
the top songs of 1946, Multiple things can be true at the same time, and historical context is important.
I am not saying it's good or bad, right or wrong. I am just saying that it doesn't exist in a vacuum.