The fallacy here is that you assume organizations exist. They do not. An organization is simply an aggregate of individuals. "The Catholic Church" does not really exist. It is just a word we use to describe a large grouping of people behaving in a certain way. Groups are nothing more than collections of individuals. The Catholic Church is evil because the individuals making it up are evil (through either action or inaction). Groups may be prescriptive in that peer pressure or coercion causes members to behave in a certain way, but ultimately they are descriptive.
Although truly evil people must take some blame for swaying others to evil, they only ever succeed when people blindly follow them.
For clarity's sake, I'm going to directly state my argument: the blame for the evil of religions, much like the evil of governments or businesses, lies more with the individuals and the portion of the general populace who blindly and/or illogically believes what they proclaim, than the instituion itself.