I obviously haven't seen the ST:TNG episode that you reference, but from the sound of it -- yes, it sounds like a valuable allegory by showing an inversion of heterosexual privilege. I believe the movie "White Man's Burden" was trying to do the same thing. But those are storytelling devices and learning tools. They aren't proposing that we, as a society, literally put those inversions into practice.
Some people have "deaf ears" when it comes to logic and discourse, but, as you point out, the storytelling makes the difference for them. Some people also have "deaf ears" when it comes to either approach. When the exercise involves role-playing or storytelling, it always requires context and nuance to accompany it...or you will fail in reaching the people whom you need to reach. There may very well have been some of that in portions that were edited out of the Oprah episode or Ms. Elliott's campus instructional session...but I didn't see it.
We can't really know what happened after the cameras stopped rolling, can we? The only way we can evaluate that is to continue the discussions. Maybe I'm wrong about Jane Elliott, and she is totally willing to have good-faith dialogue and give-and-take exchanges with participants of her sessions? But, from those two videos you'd linked, that didn't appear to be a part of her teaching style. What you describe as her merely making people "uncomfortable" is what I find to be a "This-is-my-playpen" / "It's-my-way-or-the-highway" narrative of arrogance present in many corners of academia.