I don't tend to see the problem in quite those terms, although I think we are describing similar concerns.
The problem, at least with Christianity (as I see it, from the inside), is that we confuse the institution with the belief system. The institution is, of course always looking for ways to ensure its own perpetuation: obtaining financial commitments, recruiting loyalists, and frequently choosing expediency over principle. The church is potentially an instrument of God's grace to man, but it stops being that and starts to corrupt itself whenever it forgets that its primary purpose is not furthering its own existence.
Its the commitment to the institution, rather than the belief system, that has created most of the problems. That's the basis of the whole science vs. faith argument: evolutionists (people who added a non-scientific argument over the Bible to Darwin's valid theory) attacked the institution, and creationist Christians committed themselves to defending the institution by ignoring reality. Anyone with a lick of sense, on either side, would not tie themselves to the idiotic notion that the Biblical creation story was told or written by people who intended it to be taken literally.
Worse yet, once they care more about the institution than the beliefs, people become vulnerable to those who hypocritically exploit the institution for personal power or wealth. Ripoff TV evangelists are one such type, but politicians who lead insane, bigoted attacks on families over "defending traditional marriage" are another.
But it isn't just religion that gets used this way: any sort of allegiance that is tied to an artificial construct can do it. Sports hooligans demonstrate a basic form of this aggression.
As has been pointed out, atheism is headed the same way; it's becoming, for some people, just the sort of religion you fear. Sam Harris, in "The End of Faith," approves of the idea of killing someone for what they believe (forgetting that it can't really be done; the closest we can come is to kill someone for what we believe they believe). Richard Dawkins is openly and avowedly a proselytizer for atheism, yet he opposes people teaching their values (unless they are also his values) to their children--a position that lines him up very nicely with Stalinist views on education.
Religion ought to be a framework for responsible living. Yet we must be on our guard to keep it so; if I were willing to just take my pastor's word (I assume you didn't mean "pasture"), I'd have been one of those people serving the institution instead of my beliefs, for about 15 years now. But it was my beliefs that saved me from that; that's why I have them.
Religion is the antidote here. The evils that you and I describe are not really derived from religion; they are derived from its corruption and manipulation. Christianity looks to a founder who spent a lot of time criticizing religious leaders, and was in a lengthy Jewish tradition of people who did the same thing. Atheism is now headed toward needing that same capacity for internal criticism.