Great post! I think that SMTs are potentially the solution to this. SteemIt.com is just the initial proof of concept site built around the Steem platform, but the idea has always been for other more niche communities to be built on top of it, separate from SteemIt.
SMTs will not only allow this, but also allow more control over the distribution of the Tokens, and therefore control over moderation, to the community creators.
The problem will never go away, but hopefully in the future we will be able to pick and choose which Steem-based communities we want to be a part of based on whatever criteria you want, one of which can be how open the community is to different points of view.
This is one of the biggest things I look forward to with SMTs, and I hope to create one or more such communities myself if no one else does it first!
I hope you're right and it will make it better