Their message were also rejected in some countries like mine. In Indonesia, Lightyear wasn't able to show because of it, and especially we are a religious country (not supporting but not against it either). And when the country asked if they can cut just that scene, Disney didn't want to. Thus, the whole movie is blocked and hurting the box office.

As you said, perhaps it kind showed they were lacking storytelling back then. Now that Bob Iger is back, perhaps things will change. Fingers crossed.