I think students should be taught what we are certain of and why and also what we cannot be completely certain of and why.
A discussion of the latest research into the origins of life may well be appropriate. I would also suggest a brief discussion on science from a historical perspective as a search for explanations of the unknown with a long a distinguished record of providing answers to the supposedly unknowable eventually.
The only reason for hiding areas of uncertanty is a fear that non science will be allowed to creep into the curriculum the moment a weakness is identified. I agree this is a danger but my preference would be to meet it head on rather than try and sweep anything under the carpet.
Show why the religious alternatives are non scientific and why the fact that science cannot fully provide answers (yet!) is no reason to jump to non scientific alternatives.
Am I being too idealistic? Would love to know what a real teacher in this position makes of it all?