So I decided to do some experimenting to nail down what was the problem:
This video should show what went wrong, and the impossible speed the passenger segment accelerated to.
From some forum threads that I've taken a peep at, it seems that sometimes, the physics engine dislikes it when saving and loading, so I decided to test that hypothesis, where I would not recover either craft until both have safely landed, after my command pod landed, I zoomed out to look at the passenger segment, which has its chute deployed, and is moving at such a snail's crawl that it could not have exceeded the Mk1 Crew Cabin's 40 m/s tolerance, yet that craft somehow exploded upon touching water, but even strangely, even though it contained four tourists, only one was considered dead by the contract tracker, with the other three being presumably pushed back into the astronaut complex like before.
So I loaded back and decided to adjust the parachutes so that the crew cabins would splash down first (deploying at an even lower altitude), and somehow that made them splash down fine, and was recovered just fine via the tracking station, completing the contract. I did not dare to load into the craft to then recover it in fear of the sudden acceleration happening again.