Church Bans...

These are another two words that I do not understand their ability to be linked together. In a news report today,
Priest Bans Autistic Boy From Church
Mom Told She'd Be Sent to Jail if She Brought Autistic Son to Church
I do understand concerns of safety, I want to recognize that the truth probably lies somewhere between the comments of the church and those of the family. But, mostly this in one incident within a line of the church bans...you fill in the blank. The church banned colored people, gays...
But these two just don't fit together to me. The people 'the church' tends to ban are exactly the people that Jesus himself worshipped with and taught. He didn't sit up in his suburban pulpit, surrounded by posh facilities and protected by security guards. He hung out on the beach, in the garden and his disciples slept when they were suppose to be keeping watch. I'd love for someone to take up, Jesus wouldn't have had to die if the security had been better in Gethsemane.
As someone who is a part of the protestant church but does not always agree with it, I do appreciate the last line of the article, a quote from the mother. "The church isn't bad," she said. "But it's what some individuals do within the church."