This is a great example of the kind of trade-offs you find in public health decision-making. Folic acid prevents birth defects, but it may be causing bowel cancer. In an ideal world, you use data to decide what to do – look at the frequency and severity of birth defects in a world with no folic acid fortification, and compare that to the extra cancers resulting from the fortification. The you choose the option that leads to less disease.
In the world we live, there probably isn’t enough data to make an informed decision, and there will be political pressure involved in the decision as well.