Either way why teach an unproven theory as FACT? Give both options, and let the students choose for themselves. Can you imagine if only Liberal politics was taught in school as the "appropriate" way. School is to educate youth on all options out there based on the current knowledge we have. Do not limit their choices because you do not agree with them. You atheists are "free thinkers"....so let them think freely.
As far as prayer goes, i say let the students come together to pray if they so choose. Let them give thanks over their meals if that is how they were raised. The only thing that should be restricted is prejudice against anothers beliefs.