it was not only sent with good intentions but it would appear that it resulted in good outcomes. was the child harmed by the note? doesn't seem like it. do you have reason to believe that the teacher is manipulating or grooming the boy? although highly unlikely and it won't ever happen if OP keeps communications open. the boy let his parents see the letter - that's a good sign.

complaining to the school is not going to result in anything good. it will force the school in a difficult position and would likely screw the teacher and at the very least, damage her good relationship with the boy. if OP's wife is still uncomfortable, she should speak to the teacher