The vaccine controversies page, for example, notes that some people think vaccines cause autism, but also prominently quotes someone calling the vaccine-autism connection "perhaps, the most damaging medical hoax of the last 100 years". At no point does either the vaccine or vaccine controversies article deviate from the dominant viewpoint that vaccines do not cause autism.

This is very different from the numerous attempts to edit the page vaccines to say that vaccines cause autism. That is what we'd be allowing if we say that articles must present opposing viewpoints when there is controversy. Do you really want the vaccines page to present that as a valid viewpoint?

However, I'm saying, the alternative, where treating every viewpoint that exists as worthy of inclusion, is worse.

Majority opinion isn't always right, but Wikipedia isn't well suited for solving that problem. This isn't speculation: it wasn't always this way, but the rules were made because people were flooding Wikipedia with all the insane things people believe. I've never been an active wikipedia contributor, but I've used the site long enough to remember this.