People don’t like to be confronted by their biases and will get defensive. That’s how I saw Schulz’s reply, especially since when he introduced Franklin, he got in a spot of bother over it and probably thought, “Hey, I’ve done my bit for civil rights!” The Wikipedia article on Franklin has more on his introduction in 1968. I can imagine Schulz thought he was well-meaning with that comic. But he didn’t get that the “punchline” is insulting and condescending.
There’s also the questionable clip from the Thanksgiving special. When Franklin comes over for supper, all the kids move to the other side of the table, and Snoopy too. Sometimes discrimination is so casual we don’t see it until it’s pointed out. I never noticed it myself, and I’ve seen this show almost every year for 30 years!