The Possible Spread of Conscience Clauses?

I was reading this about a possible conscience clause in the US military:

Some House Republicans are pushing for inclusion of a “conscience protection” clause in the final version of Pentagon budget legislation that could enable discrimination against gay service members, according to LGBT advocates familiar with conference committee negotiations.
The measure could be made final as soon as today.
Two LGBT advocates, who spoke on condition of anonymity, said House Republican conferees working on the final version of the fiscal year 2013 defense authorization bill are pushing for language along the lines of the “conscience protections” in the House version of the legislation under Section 536. One source said this language is “very much in play” for being in the final version of the bill and is one of the final issues yet to be resolved as conferees wrap up the legislation.
Under the language, the U.S. military would have to “accommodate the conscience and sincerely held moral principles and religious beliefs of the members of the Armed Forces concerning the appropriate and inappropriate expression of human sexuality” and may not use these beliefs as the basis of any adverse personnel action or discrimination. Additionally, it would prohibit the U.S. military from taking action against military chaplains who decline to serve a particular service member based on religious beliefs.

It's hard to know if any of that is more than rumors at this point.  But it suddenly struck me that the concept of a conscience clause can be used far outside the topic of abortions and contraceptives in health care!  A conscience clause could legitimize any kind of discrimination, anywhere!  How very neat!

For instance, employers could say that they cannot hire women because taking women out of their homes is against their conscience.  Or employers could say that they need to hire workers of only one race because their conscience doesn't allow miscegenation.  And think of what scope religious beliefs would give to discrimination!  A very strict Muslim would oppose any mixing of the sexes at work or at school.  And so it goes.

Something so innocent-looking and so much a problem only for those "baby killers" can travel far, grow big and stand tall against the idea of fair treatment.

Sure, I'm going to the extremes with this post.  Still.