It doesn't sound like it 'tears' molecules, it mearly causes polar molecules move in a swaying pattern.
Another note is that I do not believe that on that scale friction acts as a notable force. Rather the motion of the particles heats the food, not friction. You know that gases move faster then solids right?
Again, this motion 'might' cause weak bonds to break, but those would have broken in the digestive system anyways.
It makes more sense, practically, that there was a chemical reaction with the ingrediants in the babyfood rather then a microwave breaking a few weak bonds to form a nevergas.
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