I’m not sure that argument quite works, since the Bible is primary source material, and would be a perfectly legitimate source for certain types of historical arguments. For example, if a student were writing about a topic along the lines of “What roles did women play in early Christianity?” it would probably be a very useful source, if read in the right way.
So I’d probably tell the student that if they are going to use primary source material, they have to treat it as a text whose claims need to be analyzed and examined critically, with an eye to who wrote it, when it was written, through what channels the author would have known about the events described, and what the author’s purpose for writing and biases might have been, rather than accepting everything the author says at face value. If they’re not prepared to do that for any given source, they shouldn’t use that source. I would also point out that academic writing needs to be persuasive to any educated reader, including people who do not share the author’s religious beliefs.
Disclaimer: I’m neither a historian nor a high school teacher, and I have no idea how ready high school students are to take in this set of ideas, but this is pretty much what I tell my freshman comp students. (They don’t always get it, either.)