The idealistic main aim of any science education should be for students to understand the nature of scientific investigation. Long after the facts, figures and specifics of a theory are forgotten students should still be able to recognise scientific research as distinct from the likes of astrology, superstition and (dare I say it) religion. To understand that a search for truth within an objective reality is what underpins the methods of science is key. In the specific area of biology I do not believe this is possible without discussing, arguably, the most far reaching theory in science - namely the theory of evolution as describing the formation of species from common ancestry - in the broadest of terms.
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?