@time-ex:
In both of the B747 disasters cited (thanks for that, by the way -- I was not familiar with the China crash), the repairs were NOT in accordance with repair procedures approved by Boeing, even though in the JAL case the incorrect repair was made by Boeing technicians.
Modern aviation has a long history of really extensive airframe repairs, including components as fundamental as wing carry-through structures. To my knowledge, the safety record of such repairs is fine, when they are performed correctly.
My expectation (God knows, I could be wrong) is that any team conducting a repair on this burnt 787 -- if the ship will indeed be repaired -- will include people who know the heart-breaking history of the JAL crash. It was a massive loss of life that was Boeing's fault, the worst nightmare for most people in the industry, and one not readily forgotten. [Anecdotally, in the mid 90's I was talking with a Boeing-Seattle engineer who referred to the Associated Grocers' B-29 crash from 50 years earlier ... not only before his time, but before he was born.]
If Boeing makes/supervises a repair to the 787, and they aren't truly able to assure the safety of that repair, then what is their understanding of the materials and processes? How could they make an airworthy ship in their own factory, without such understanding? Carbon composites are not magical/mystical materials. People have been making lots of things with them for a long time, breaking those things, and repairing them. It is precisely BECAUSE these materials are so well understood, that the naturally cautious air transport world has by stages introduced them into airframe structures.