A NY Times article this morning, regarding the order President Obama plans to sign on Monday prohibiting anti-LGBT discrimination by federal contractors, notes that "the order will also, for the first time, explicitly protect federal employees from discrimination on the basis of gender identity, officials said." (As I understand it, transgender workers are considered to be covered under the "sex discrimination" portion of the executive order protecting federal workers from discrimination. This seems to be a little unclear, however. The new order will only affect employees of federal contractors, and not federal workers themselves.)
While there is no new religious exemption, the article notes that "[r]eligious groups that have contracts with the federal government already have a limited exemption from existing anti-bias rules, based on a 2002 executive order by President George W. Bush. That directive allows them to factor their religious beliefs in their employment decisions.The directive will not change under the new rule."
NY Times: Obama to Issue Order Barring Anti-Gay Bias by Contractors
WASHINGTON — President Obama plans to sign an executive order on Monday that protects gay, lesbian, bisexual and transgender employees from discrimination by companies that do federal government work, fulfilling a promise to a crucial Democratic constituency, White House officials said on Friday. But the directive will not exempt religious groups, as many of them had sought.
The order will also, for the first time, explicitly protect federal employees from discrimination on the basis of gender identity, officials said. Federal workers are already protected based on their sexual orientation.