To launch himself forward he has to launch the train backward and the train likely doesn’t survive that

Is he canonically heavier than the train?

He can ‘run faster than light’, or at least, it’s safe to assume he is faster than all human technologies of mobility in the context. All he has to do is accelerate to a speed, taking into account the distance required to decelerate to a non lethal speed to intercept the kid.

It’s basically this - the deceleration required to reduce the speed to one that is either a full stop or at least a non lethal one at the point of impact can, by definition, instead be imparted to the kid. A hypothetical person in the first engine that supes is acting on is experiencing the same deceleration as would be required to accelerated the kid during intercept.

The kid intercept is simply a more efficient way to address the situation, albeit a less dramatic one.