I realise that I may be a little late to the party, and hope that this doesn't count as a thread necro.
I'm not convinced that science and religion are incompatible. A lot of great scientists, including Newton and Einstein, were able to reconcile the two in their personal beliefs.
While I'm not religious myself, I'd argue that science and religion speak to different domains. Science encompasses all that can be formed into a "testable hypothesis". The concept that "There exists a supernatural entity, undetectable by normal physical means", is not a testable hypothesis, therefore it's not a scientific belief. The tools of science are not useful in answering this question. In the same way that there's no scientific answer to questions like "What's the best way to live my life?", or "How should I treat other people?". To some extent, we can contort these into semi-scientific questions, like "How should I best interact with people in order to maximise by financial income?", or "How should I live my life in order to avoid suffering chronic disease?", but the original questions as formed fall more into some sort of "spiritual" or "religious" box.
A literal interpretation of the bible certainly clashes with science, as ERDoc and others have given examples of. The ideas of resurrection, or bringing the dead to life (at least 2,000 years ago!), would require a substantial adjustment of modern science. They tend to fail "Occam's razor", the concept that the simplest given explanation that accounts for all aspects of an observed phenomenon is most likely to be correct. The hypothesis that we live in a world that's 6,000 years old which has been elaborately constructed by some form of supernatural deity to appear older than it actually is, and that this information has been preserved by a select few since antiquity, is certainly more complex than the currently accepted scientific explanation. But it also remains fundamentally untestable, placing it outside of the realm of scientific enquiry.
I think that ultimately, science and religion cover different spheres of knowledge, and are different means of interpreting the world around us. THey have their inherrent limitations, but most of the problems occur when they try to encroach upon each other.
To chbare - if you have a student who is losing religious faith because they're learning more about science - if this person is an adult, I don't think you have any obligation to withhold your personal opinions. If they're foolish enough to let an instructor define their world view unquestioningly, then they obviously weren't going to get very far in terms of rational enquiry. I would suggest prefacing anything you state with "this is my personal opinion", or providing an explanation as to the limits of current knowledge. I suspect that you already do this.