The stated intention of the health care bill is to provide affordable coverage to all Americans. It can be done in a way that individuals have access to all services, without objectors providing them.
In essence, it is as simple as setting the criteria based on a total cost of health services per individual each year. An independent body can compile statistics on the average incidence of various types of services over the past year, and employers would be responsible for providing a plan that keeps the average cost of obtaining such services under a target number (and set cost caps). Faith based orgs can exclude contraceptives but provide benefits such as lower co-pays to offset the total cost so that individuals have more money in their pocket to make their own choices of morality.