My guess is that after the burn he got over contraception and “Freedom of religion” that Obama’s not going to go tell government contractors – many of whom are religious organizations and who were specifically told they’d be allowed to discriminate against LGBT’s with federal money several years ago – to stop discriminating. At least not in an election year.
And people won’t get the distinction between telling a church not to discriminate and telling a religiously affiliated government contractor not to. Catholic Charities, which raised the biggest stink about being told to cover contraception, receives most of its money from the federal government, often in the form of contract work instead of grants. Obama won’t tell them to stop discriminating against gays (which they openly do) in an election year.
The employer’s rights to tell their employees how to use their genitalia, not the employees’ freedom, is more important right now, and the sorts of people who make major contributions to campaigns want to keep it like that.