For fuck sake - problem is not in religion but in people exploiting it for their needs or justification.
I think that I'm atheist, but mostly I just don't give a fuck about religion.
If people are good and have their religion just to give meaning to their lives, it's all grate by me. I have Islamic buddy from Egypt (live in Turkey) and he has view of Islam that actually looks appealing to me. Islam doesn't approve violence or any kind of harm and those that portray it as such, is not considered as TRUE Islamic believers.
Same was when Christianity went on holly war - meaning behind wasn't spreading religion, but gaining wealth.
Because religion give such big influence on people (giving reason for their life and shit) there are people that use it to push people around, even brainwash.
So, we shouldn't pass judgement on people for what they believe or think, but what they
do, is what you're saying? If so, I tend to agree; but we have biases all over the board on that stance. Thought crimes are very real, they just seem to apply to particular groups.
Take National Socialists/Neo-Nazis for instance. There are many who just agree with the philosophies and go about their day as functioning individuals, but the moment we find out what they think, the beliefs they ascribe themselves to, we're disgusted, and we're not shy about letting them, or anyone around us know.
There are misconceptions about a lot of belief systems and how they effect the average person, but society often nit-picks who's demonized based on sole principal. The "No True Scottsman" thing doesn't apply to Nazis, they're just Nazis, and they're wrong and bad. This is not true of any other political view, all others are given plausible deniability.
On that note, I also do not see a difference between religion and politics. Militant Atheists have this nasty habit of scrutinizing holy texts while the religious extremists are busy vying for the domination of the world. The God Question is rather old-hat at this point in history; belief or disbelief in the supernatural basically doesn't matter in the natural world. It's unfortunate that Theists and Atheists alike rarely come to that realization.
I think the short version of my point is that ideas are dangerous. If they've been proven to be detrimental on a massive scale, they should be removed from any amnesty. Some ideas are just poisonous, even if they don't kill certain people.