I don't know anything about this case, but the science class incident sounds pretty suspicious to me. Assuming that what the science teacher is alleged to have said is close to being accurate, you have to imagine why he said it.
Why would the student have been arguing about the Bible in science class? The first thing that comes to mind is that the student was using the Bible to deny science. Maybe he was claiming that the Earth is only 6,000 years old. Maybe he was claiming Noah's flood was a literal account of a worldwide flood.
Who knows, but conservative Christians raise ludicrous claims like that all the time. Science class is no place to raise superstitious beliefs and discuss them as if they have any semblance of truth or are worthy of respect.
If the science teacher did indeed shut the student up, then the science teacher was right to do it. The Bible is not a science book. Vast numbers of Christians don't believe in the literal historical truth of the creation account, or Noah's flood, or whatever else this kid might have been asserting.
It's not persecution to set science class aside for actual science.