What I’m not clear on is, would the passengers feel like they just decelerated by 200+ mph in an instant?
More likely the turbulence and vortices in the demarcation zone between the jetstream and the different air current the plane enters would jostle and toss the passengers around more than the deceleration would.
From the article, it said the 787 was cruising at 35,000 feet. Seeing as the 787 was built to cruise close to 40,000 feet (above most traffic and weather) I daresay the pilot or company flight planners deliberately asked for a lower altitude based on expected wind conditions. I bet many other airlines were doing the same, leading to a very busy jetstream highway that day!
I mean, the opposite effect is well attested to - you fly along with a headwind (and sufficient airspeed), then comes along a sudden tailwind, and your airspeed drops sufficiently that you stall, or at any rate descent. Wind shears, often associated with cold fronts or thunderstorms.
Maybe a) mach 1 is further from cruise speed than cruise speed from stall speed, and b) drag slows down the plane more effectively and quickly than the engines can accelerate it.
That could explain why wind shear has and does lead to stalls, but not to sonic booms/structural disintegration.