Oxygen, I think is the major factor. As long as the salmon is frozen and sealed, the bacterial growth is slow/spores remain inactive. When thawed while sealed, they are all trapped in there without oxygen and become active with the increased temperatures. According to some quick wikipedia search, it is the germination of spores into bacteria that creates the neurotoxin. The absence of oxygen is a requirement for the germination, so it promotes neurotoxin production. Releasing the salmon from the package before thawing lets oxygen in, thus they won't become active as the salmon thaws, since oxygen slows down the bacterial growth.

Not an expert so take it with due caution, but as I recall when canning things like meat and I think tomatoes you have to use a pressure cooker rather than just boiling water to get the temps past 100 C, so I guess just cook the shit out of it?