Assuming the claims are valid, and the quotes aren't being distorted, taken out of context, or lied about, this is a legitimate claim. IMO, telling his class that they shouldn't be Christian is just as bad as telling them that they should.
However, it's definitely not cut-and-dried. I can easily see where a discussion on the use of Christianity (or any religion, really) to manipulate the public would lead to such statements. I can also see a Christian student wanting to "get" an outspoken, atheist teacher and digging for ways to get him fired.