Run by Humans [NSFW]

Beth: Anyway, Magdalene Asylums were an Irish-Catholic thing, spiritual sanctuaries for "sinful women." You know...prostitutes, abuse victims, flirts.
The hilariously misnamed Sisters of Mercy would lock these girls inside sweatshops, force them to work under the whip for their penance.
And this wasn't the Dark Ages, mind you. I found out my biological mom died in one of these hellholes in fucking 1989.
So you don't need to tell me how screwed-up the church was, all right? You're preaching to the goddamn choir.
Amazon 1: If that's true...then renounce your God.
Beth: Go to hell.
Amazon 1: Renounce your allegiance to this patriarchal hate machine...or I kill you where you stand.
Beth: Patriarchal? Did you hear anything I just said?
The church wasn't fucked-up because it was run by men, it was fucked-up because it was run by humans.

- Y The Last Man #25

by Brian K. Vaughan and Pia Guerra

This. That last line. I love that last line. Yeah, it may be profane, but the sentiment is for sure spot on. Have males committed some heinous atrocities in the name of God? Absolutely. But so have women. So have any slice of the population. Males have likely committed the most, though that's due to them tending to have the power and therefore the opportunity to abuse it. I'm not trying to justify this. I'm saying whatever group of humans hold power in the church, the church will still do messed up things. Because it's run by humans.

Humans mess things up. That's why we needed a savior in the first place. This is why it never makes sense to think that if we just had a more "Christian" organization in power then all these troubles in the world would go away. A Christian administration in power can be just as corrupt as a non-Christian one. Look at ancient Israel in the Old Testament. That was a messed up government. It seems like most of the OT is spent chronicling just how messed up it was. And they even had the advantage of God directly interacting and intervening with it on occasion.

The church, in concept, is a great idea. Our execution of it has never been all that great, though. We're human. We fail. Again, it's why we needed a savior. It's why we still do.