Does Obama's latest executive Order endanger religious freedom?

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President Barack Obama signed an executive order Monday banning federal contractors from discriminating against employees on the basis of sexual orientation or gender identity.
Despite calls from religious leaders, faith-based groups will not be exempt.
"Thanks to your passion and advocacy and the irrefutable rightness of your cause, our government -- a government of the people, by the people and for the people -- will become just a little bit fairer," Obama said.
Gay federal workers are already protected from workplace discrimination by a Clinton-era order and Obama's action extended the protections to shield workers from gender identity-based discrimination.

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President Obama, resisting calls from several prominent faith leaders, will not include a new exemption for religiously affiliated government contractors when he issues an executive order Monday barring discrimination on the basis of sexual orientation and gender identity, the White House said Friday.

Obama announced last month that he would sign such an order after concluding that Congress was not going to act on a broader measure prohibiting discrimination based on sexual discrimination or gender identity by companies.

White House officials said Friday that the new executive order would not include such an exception. But Obama will preserve an exemption put in place by former president George W. Bush that allows religiously affiliated contractors to favor employees of a certain religion in making hiring decisions.

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the link bellow is a fox news opinion article, I know it is very bias to the right but it is one one side of the issue.

LINK

I want to find an opinion article explaining the other side of the issue but so far in my searches I have come up empty, probably to early, and the left will focus on the victory for LGBT groups and not how it effects religious liberty.

so thoughts?