If we take your argument to absurdity though and say that 'we should never suppress ideologies because we cannot know tolerance vs intolerance', then that leads to things such as allowing cults to operate unhindered, groups that plan murder in the open and so forth.

For example, the KKK. What would be the solution to solve that, if not for society to take an active stance against it? Should we let them continue on their merry way because it's impossible to determine intolerance and morality is complicated?