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We have a representative democracy. We do not, as a country, make decisions directly but select people to make those decisions as proxy.
Everything our government does has a moral component, and therefore expecting our elected officials to not engage in moral calculus is contradictory to our method of government.
Whether life becomes protected at conception is not fundamentally a religious question (there are many atheist pro-lifers), though it is a question addressed by pretty much every religion. What it is not is a scientific question. There is no absolutely right or wrong answer.
If legislation was passed and signed that made it illegal for any stem cell research to be done then I think there would be a stronger argument for unacceptable moral dictation, but that is not what has been done. There is no right to federal funding. I disagree with his decision to veto the bill but it is neither surprising (it isn't like we didn't know the man elected would take a position against fetal stem cell research) and within how our government is designed to work.
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