Let me just get this straight. Are you honestly arguing that any good done by the church is actually done by individuals yet any bad done by the church is due to the church itself? Because this argument in reverse is used to defend religion and is a bit rubbish then too.
To be fair,
The Church doesn't do anything - it simply preaches a set of values (which have changed over time), some of which had have a positive impact others a negative.
Negative & positive things are done in the name of & against religion from all sides, but what we should be doing is challenging the negative things.
I don't think the "promotion of charity" should be our highest concern, but the promotion of homophobia, backwards scientific ideas & the covering up of the molestation of children from various religious groups.
The problem with religious values is that religion can make a good person do terrible things - as if our data in invalid our decision making process is also.
To use an example,
Mentally ill children with tourettes.
A loving family if they genuinely believed in possession would think drowning the child would save it's eternal soul.
In the eyes of the parents this act is moral, because they are acting off a flawed view of reality it stop them from making a rational judgement.
Add in modern understanding.
Which now indicates that tourettes is an inherited neuropsychiatric disorder,
The behaviour of the adults in question would now change to a caring moral duty, all that has changed is the data & information to act off.
Religion overall denies this kind of advancement at every turn, morality isn't some fixed system in which we call all follow mindlessly, but a constantly changing set of values based off information provided.
If it was determined that child abuse was 100% the cause of all murder (not really this is an example), would we then view murderers in the same light?, would we stop demonising them & put efforts in place to ensure they don't develop?.
Obviously, that's a made up example - but that kind of progression isn't possible with black/white morality which religion promotes.