Despite everything, I still don't think the solution to the 737 MAX problem is to start over. The base problem that Boeing has its actually their terrible engineering culture, the one that values shortcuts and profit over thoroughness and safety.
Even if they started from a blank piece of paper, they'd have that engineering culture problem (and to be fair, it is far more likely an engineering management culture problem), and they'd still turn out a design that kills people.
So it's not if they should "start from clean" but just accept the need for the new certification and then do the changes that are really needed. It will be less profitable for Boeing but it righly should be this time! They are killing people otherwise.