From the Article:
"President-elect Donald Trump is vowing to block federal funding to Sanctuary cities, but the incoming commander-in-chief may find it tougher to take on another powerful protecter of illegal immigrants -- sanctuary churches.

Hundreds of houses of worship around the nation have pledged to provide safe harbor to illegal immigrants facing deportation, as have cities such as Chicago, Los Angeles, Philadelphia and New York City. While Trump may relish a policy and funding fight with the leaders of Democratic strongholds, imposing his administration’s will on churches could be another matter.

“There is a long tradition in American law enforcement of not breaking into churches in order to arrest someone unless the person is wanted for an act of violence,” Fox News Senior Judicial Analyst Judge Andrew Napolitano told FoxNews.com. “In order for the police or for Immigration and Customs Enforcement to enter a church against the will of a priest or minister who is running the church, they need an arrest warrant for a specific human being –short of that, they’re not going to go in there.” "

I have always support Freedom of religion and the right of Freedom of Speech. However to tradition of Sanctuary in churches is not one that I support.By harboring illegals they are encouraging contempt for the law within the community and especially within the illegal immigrant community. Go to church and be safe from the law.
If you are in violation of the law, you should not be exempt from enforcement simply because you go into a church, mosque or synagogue. (I'm not sure the last two provide sanctuary.
We don't have a system like that found in "The Hunchback of Notre Dame". Ours is more of the I got here illegally now I'm going to hide out for a while. type. and it I hit or miws. No denomination that I know of has a specific article of Faith specifying the right of Sanctuary.
A very unpopular solution would be to revoke the tax exempt status of any church that provide sanctuary to illegals. I am not advocating such a step nor would I approve of such, but I've heard a few whisper it. (They also don't support Tax Exempt churchs period.)