According to Forrest Wickman at Slate, Beyonce's apology (quoted by Wickman) says in part:
The song ‘XO’ was recorded with the sincerest intention to help heal those who have lost loved ones and to remind us that unexpected things happen, so love and appreciate every minute that you have with those who mean the most to you …Wickman says the song is about mortality, not just "a failed relationship" as some news outlets have claimed, and the difference puts the sample in the proper context for it to make sense.
I haven't heard the song and I'm not going to, because based on her intentions I already know she fouled up.
The Challenger disaster wasn't her tragedy. If she had lost a loved one in the explosion, maybe she'd be entitled to write a song about that.
But she didn't lose anyone in that tragedy. The song isn't even about it. Taking her at her word, the song just abstractly urges us to make the most of our time with our loved ones. That's nice.
Unfortunately, she decided to give her song some emotional heft by referring to a very non-abstract disaster. And that was crass.
Beyonce, your intentions are irrelevant. Using the Challenger audio clip was exploitative. Some might even say it was cruel. There were a million other ways you could have driven home your point. Why the shuttle explosion? (The cynic's answer: because there was a readily available audio clip. Duh.)
Admit that you made a serious error in judgment, remix the song without the clip, and move on.