One more thought - how far does this go? A registrar whose religious beliefs do not allow marriage after divorce? A GP who doesn't approve of the homosexual lifestyle? A pharmacist who does not approve of contraception? Naming ceremonies for the children of same sex parents?
In conservative areas where religious groups hold great sway and where perhaps services are thinly spread (e.g. rural areas) the service that the employer is required by law to provide (or wishes to provide in a certain manner - e.g. with an assurance of non-discriminatory attitudes from all employees) will be severely hampered and such things as roster co-ordination and annual leave requests become a nightmare as we all have to work around bigotted staff, immune from sharing their employers' duty under the law to avoid discrimination in their service provision.
Some further reaction below:
Louise Ashworth God is above employment law and More on the Registrar
The Observer has Civil rights must trump faith: