From your initial post, you were concerned that this would be a safety issue, cutting and rewelding new parts onto the body, while if done properly can be just as good as new from factory, if it's done right.
The problem is... will it be done right?
I don't question that their body/frame shop is not up to the job there are many master body/weld/paint people out there, I question your peace of mind.
You stated, (as have others) that you paid for a new car, you should get a new car if it's being offered to you.
Will you be 100% comfortable with living with the car that you knew came from the factory with a defect? Will you be 100% sure that in the case of a horrendous and unfortunate accident should it ever happen, that this car will save your life, repaired or not?
If you are unsure of that answer after a period of reflection, It would probably best to take the replacement.