At the most basic level, religion doesn't need any more influence than it already has and it is not the role of government to make it a foreign policy position.
At the level your are speaking to, nations make their own decisions about these things - and, as the article stated, the US doesn't have clean hands when it comes to dealing with those nations that have less than sterling records of religious freedom. When it stands to benefit (ex.: Pakistan), the US is more than happy to turn a blind eye. That makes our foreign policy utterly inconsistent on this issue - and completely toothless as a result. Better to say nothing than prove how permeable US foreign policy can be when it suits us.
If the US was consistent, I'd say we had a leg to stand on when discussing religious persecution (and only that - we have no business preaching anything else to other nations). But clearly we are not consistent in our words, actions, and policy. Given that - we need to get out of the pulpit. It is foolhardy to preach mixed messages.