Acceleration doesn't seem to matter 90% of the time in superhero universes. Also, if there was enough time to slow the train down there was enough time to get the kid off the tracks safely.

Seeing how the train engineer is just fine and not flying out of the train, the train didn’t violently decelerate. Meaning that the train stopped over a long distance and thus Superman had enough time to just move the kid next to the rails without high acceleration.

I'm sure the passengers/conductors of the train are perfectly fine with it

I’m sure the deceleration of the people on the train was healthy.

I’m guessing in this particular comic the train was some kind of empty runaway train. Just to avoid raising such concerns. Even then, it seems like there would have been a less destructive way of stopping this thing. Like maybe flying into the train and pulling some kind of brake.

Right? What's wrong with a little bit of life-threatening whiplash?

This joke was used in Hancock, car instead of boy. But a bunch of people got angry at Hancock for destroying a train rather than lifting the car out of the way.