I could literally make the same argument for Athiesm causing harm. Does that mean that I should respond to you by saying "we should destroy Athiesm?".

As I said, athiesm isn't an organized belief. People are born athiest (seeing as how your usage of "athiest" also encompasses agnostics). You only get brainwashed later. It's just illogical to group them like you can group a certain religion or sect.

Or should we realise that both of our religious-based beliefs should be tolerated.

I tolerate religious beliefs that don't believe in the concept of eternal punishment, or don't promote the idea that some groups are in any way "lower" (including "more sinful" or "less holy") than others. Most kinds of Judaism, for example, they're fine, they don't have eternal damnation, the entire idea is to be good in your Earthly life. But even that kind of religion eventually branches off into e.g. maniacs that believe the same type of garbage that Christians do, or a theocratic Israeli government subjugating others...

A religion based on a benevolent God kind of falls apart when you consider it chooses to let the majority of people suffer, or it chooses to let the majority of people burn in Hell because they were born into and lived their life in an environment without that religion, or chooses to let people burn in Hell at all. And you save yourself by... believing in one specific random thing that happened before your entire traceable family tree even existed that is just one of many and could easily be the "wrong" one? In the case of Christianity the only thing you can bring in is the "Satan" argument or the "but he gave us free will and then Adam and Eve ate the apple so he makes us all suffer now!". That is just absurd, and it inherently promotes the idea of punishment as a core of the religion – the religion is based around punishment.

Otherwise – I'll tolerate religion about as much as I tolerate an Anti-Vaxxer's beliefs or a Scientologist's beliefs or a Flat Earther's beliefs or the beliefs of someone who follows Greek Mythology. Just infectious, harmful brainwashing that shouldn't be promoted or enabled by the jurisdiction as it is now.