I'm sorry, but there really is no way both mages and templars can coexist peacefully. It's human nature.
In real life, humans will never fully accept everyone for who they are. Mostly because many are the people in power who don't accept everyone for who they are. Only few world leaders are accepting of everyone. Barack Obama, for example. As fair as he is, there are people who despise him, and consider him a terrible president for the United States... despite the "good" he has done.
Those in power will fight back when their power is threatened, whether their actions are justified or not, or fair or not.
As long as there are people who hate for hates sake (or whatever their reasons), they will continue to seek like individuals. Conversely, people who are accepting of others, seek each other out to rebel against the haters.
As long as mages and templars think themselves right, or just want to have all the power, they will never cooperate.
Even if they DO manage to settle their differences, it WILL take mass death, and possibly even mass destruction to do it.
Deny it all you want, OP.