I would worry about overpowering the frame and the brakes.
Going from a 50 to 125cc, the engine is both heavier and more powerful.
It sounds like the 50cc frame with 1 shock may not work well with an engine from a scooter with 2 shocks ?
In the long run, it is usually cheaper to replace the vehicle than to make it into something other than the original design.
And the replacement vehicle probably is more enjoyable to ride.
Anyway, an interesting question.