First, it proposes a restrictive interpretation of the right to conscientious objection within the public sector, which would be limited to "rare and specific" exemptions agreed by parliament. His stance is in accord with the trend of recent employment tribunal and court decisions but it departs from the generous British tradition accommodating conscientious objection wherever possible.
Why, for example, must a marriage registrar be legally compelled to perform a same-sex civil partnership ceremony against her religious conscience when other colleagues are readily available to do so? Protecting conscience would not imply a "blanket religious exemption based on subjective feelings" but rather a better balancing of objective legal rights.
Second, it fails to recognise that an effective right to "manifest" belief is not only individual but organisational. For many religious believers, manifestation is a corporate not a solitary enterprise, coming to expression in a wide range of faith-based educational, welfare, charitable, publishing or campaigning associations. Some operate outside the public sector while others come within its purview either through historical incorporation by the state (eg church schools, religious hospitals) or through having entered into contracts with the state to pursue specific public purposes (eg faith-based social service agencies).
But Harris wants to impose severe legal restrictions on the ability of such religious organisations to act according to their distinctive religious beliefs the moment they enter the public sector, thereby frustrating the very reason for them existing as distinct bodies rather than mere replicas of secular agencies. For example, it could have the effect of coercing church schools into hiring staff who might repudiate the very religious beliefs or moral practices defining the school's distinct identity, or of preventing such schools from teaching RE from their own perspective.
Third, it elides the distinction between a separation of church and state and a separation of religion and state. The meaning of the first is plain enough but Harris is worryingly unclear about what he means by the second. Like many who call themselves secularists, he claims to be against "banning religion from the public square", yet the tenor of this and other public interventions suggest a desire to keep it on a tight leash.