The headline and article text make this confusing, but I'm pretty sure that Stewart is saying that Apple did block him from having her on the podcast that they sponsored, not that Apple expressed any opinion at all about him having her on the Daily Show.
This is part of Apple's general heavy-handedness which caused him to quit, not an attempt to block Khan in other outlets.
There was a podcast that went along with the Apple TV show. He wanted to interview her on the podcast, not on the TV show. But the AI and China segments they blocked were for the TV show.
This is part of Apple's general heavy-handedness which caused him to quit, not an attempt to block Khan in other outlets.