UI Confusion is never "ultimately" the cause for accidentally killing people through poor operation of a $2 billion piece of military equipment. A UI may suck, many do, in or out of the military. So, training. and then more training.
I don't have a high stakes job, but if I allowed code-completion to drop tables, commit the change, delete the backups, and then burn down the building... well, that's not on the UI, that's on me.
So unless we're talking MS Word Clippy-- and I think the article would have mentioned that-- UI can't take the fall on this.
Besides: It began with the Helmsman sending all control instead of just throttle control to the Lee Helm station. That mistake isn't explained as a UI issue, it's glossed over, but everything came from that initial screw-up. Sure, afterwards there was confusion, but even then, "OMG WE LOST ALL STEERING INCREMENT THE IDIOTIC PANIC OPTION VARIABLES!" isn't really an acceptable response. How about, calmly, "Helmsman double check that control assignment if you please <insert navy jargon cliche />"