Religious freedom is the freedom of an individual or group to pursue their beliefs for _themselves_. Religious freedom does NOT give the individual or group the right to determine the beliefs or actions of others, including employees of the group.

Just as government might legitimately require religious groups that don't believe in vaccinations for themselves, to provide vaccinations for their employees, the government has every right to require that health measures, including birth control and abortion, be provided for employees of a religious group. The government is not forcing the members of the group to use birth control or have abortions _themselves_, so their religious freedom is not being curtailed in any way.