"Your country is well known for its firm commitment to equality of opportunity for all members of society. Yet ... the effect of some of the legislation designed to achieve this goal has been to impose unjust limitations on the freedom of religious communities to act in accordance with their beliefs," he told the bishops.
I can't figure out what religious belief is being squelched. Ok, the Pope believes that homosexuality is sinful, but I'll note that he isn't generally opposed to hiring sinners. Nor even opposed to hiring sinners who don't agree with him about whether they're sinners.
And I've never heard of any rule  which says that you may not hire people who don't share your religion. There's nothing in the Bible which says "Thou shalt not hire a gay accountant." 
Though I'm willing to find out if I've missed something.
 Wibble alert. Did they have accounting back then? I think the Babylonians had accounting, but did it become a lost art for a while?