The U.S. Supreme Court has upheld the Patient Protection and Affordable Care Act, drawing cries of disappointment and concern from pro-life and religious freedom advocates nationwide.

Christen Varley, executive director of Conscience Cause, a nonpartisan advocacy organization that works to secure and defend religious freedom, said that she was "extremely disappointed" with the decision.

"The first line of the First Amendment in our Constitution guarantees all Americans the right to religious freedom, as our forefathers intended," Varley said. "Now, we have opened the door to a government that sees no limit to the amount of freedoms it can take away."

In a 5-4 decision, the court ruled on June 28 that the law is constitutional, including an individual mandate that requires virtually all individuals to purchase health insurance plans.

The justices said that while this mandate does not fall within the powers afforded by the commerce clause, the penalty that people must pay if they refuse to buy insurance can be understood instead as a kind of tax that Congress is authorized to impose under its taxing power.

The decision means that the fight over a separate and highly controversial federal contraception mandate will continue. The mandate would have automatically perished if the law had been struck down.  

Issued by the Department of Health and Human Services under authority granted by the Affordable Care Act, the mandate will require employers to offer health insurance plans that cover contraception, sterilization and early abortion-inducing drugs, even if doing so violates their consciences.

The mandate has drawn widespread criticism from individuals and organizations representing a variety of religious and political backgrounds. Lawsuits challenging the regulation have been filed by more than 50 plaintiffs across the country.

Bishops from every diocese in the U.S. have spoken out against the mandate, warning that it poses a severe threat to the religious liberty of those who object to it.

Varley said that the mandate "represents an egregious affront to religious liberty" and vowed that Conscience Cause would continue working with people of all faiths to petition Congress "to overrule this devastating policy, which undermines our religious freedom."  

Critics have also spoken out against a provision under the 2010 law regulating involuntary funding of insurance plans that cover elective abortions.

This will take place through a monthly surcharge for all people enrolled in plans covering abortion.

Regulations issued under the Affordable Care Act require that the surcharge be at least one dollar per month, but they do not dictate any maximum rate, and nothing prohibits insurance companies from charging substantially more to pay for abortions.

This provision lacks a religious or moral exemption, and it forbids insurers from telling enrollees how much of their money is going to fund other people's abortions, making it difficult for them to withhold that portion of their premium.

Marjorie Dannenfelser, president of the Susan B. Anthony List, which works to elect and mobilize pro-life women, said that the Affordable Care Act was "fundamentally flawed" from the very beginning "because it makes American taxpayers complicit in the deaths of countless unborn children."

"Over the last four years, President Obama has revealed his loyalty to the abortion industry," Dannenfelser said.

"As the presidential race heats up, the Susan B. Anthony List will continue to remind American voters where the President's allegiance truly lies," she vowed. "We will not stop fighting until every U.S. taxpayer is freed from under-writing the abortion business."