Whatever I did, I'd document it.
And what I'd do depends a bit on the school - is it public or private? if it's private, is it religiously affiliated? If it's religiously affiliated, you're SOL. but if it's public, or they make a point of being religiously neutral, I'd say go to the department head. You said you recorded the lecture? Bring that with you. Point out that what's being taught is NOT history.
I can't help but wonder - is this a professor, or is this a TA or otherwise someone just teaching this class? if it's someone with tenure, not much you can do. if it's a TA or something, though, they both might not realize they've crossed a line and really shouldn't've gone there. Or the might not care because it doesn't affect them anyway.
But really. document. cover your ass. Because if it's someone that'll be vindictive, not being able to cover your ass will screw you.
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