The article isn't that complicated. He meant to say exactly what he did say.
Which makes sense, given the entire point of tolerating free speech is that people are free to say terrible things, not "moderately uncomfortable" things.
Executive summary: (1) Open societies are more innovative. (2) Silicon Valley is becoming less tolerant of divergent viewpoints. (3) This is primarily culture-driven, but will likely have an effect on innovative science, which by definition starts as sounding somewhat crazy.
As measured by what? Are there people being jailed for expressing a divergent opinion, or being refused service in restaurants/hotels/shops/etc, or unable to find employment?
For the latter point, employment, some people are likely to pick one of the few examples that routinely get reused in this discussion - such as Damore + Google, or Eich + Mozilla. But are these kind of things actually happening at an increasing rate? Because I recall similar things happening in the 2000s, and 90s, and I wasn't around before but they likely did too (and go back a few decades earlier, and it'd be saying something like "women can be engineers just like men" or "black people can be doctors just like white people" that'd get you ostracized, so yeah). So unless you have actual data showing that there has been an increase in people getting fired/being denied employment in the past 5-10 years for having divergent viewpoints, there's nothing there.
If your main measure for "less tolerant of divergent viewpoints" is "people being mean to you on Twitter", well yeah, that's part of living in an open society. In fact one could equally argue that people feeling more empowered to call out things they disagree with is the very hallmark of an open society.
Appeal to authority, but I admit he's in a better place than I to see whether it is or isn't in funding circles.
It's jail vs sacking; different aspects of the same reaction.
(Not that this reflects my opinion of Trump.)
Saying it's easier to talk about things in China vs US. I've been to China and you can get thrown in jail for saying the type of things we say re. our political environment. My friends there have to speak in whispers in public while people in SF have no problem raging about our politicians.
And saying we should "allow people to say disparaging things about gay people if we want them to be able to say novel things about physics". At its least a really poor choice of words there. The choice of words makes it sound like it's okay to stand aside while they spout bigotry. Perhaps he meant it's okay to say it, but we should argue against it - but unfortunately for him that point was not made because the intention of the article was to support free speech. Bad example.