I want to say this at the get-go before I am accused of being prejudiced and bigoted: I do not think that only atheists can do science. I do not think that only atheists can determine science policy. In searching for someone to head the NIH, such a policy would reduce the field considerably and exclude many excellent candidates that we would be justified in predicting they would do a fantastic job.
Francis Collins is not one of them. Yes, he has shown his ability to administer very large scientific projects. Yes, he has demonstrated his ability to do good science. But these are not the only requirements for heading the National Institutes of Health, the largest funding agency for biomedical research in the US. Something less well known is that it also funds research outside the US if certain conditions are met.