Earlier quoted context omitted.
I don't see how chanting for a group, without any implicit or explicit diminishment of other groups compares to hate speech against sexual minorities. Also, chants are not a company policy, it's what employees spontaneously do in their own private space, which you saw on their own private broadcast. (If we're bringing SJW approach into this, then I think you're advocating the minority (SpaceX employees) should adapt…
I too find it hard to see how so many have conflated chanting for a group, in this case the USA, as being equivalent to actively admonishing another group. The employees at SpaceX aren't burning the flags of foreign countries or otherwise disrespecting or mocking them, they are simply expressing pride in the nation that many of us view as playing an instrumental part in our success. I also don't know what could be do…
We get to see a sometimes-messy slice of the culture, but we're also seeing how real engineers celebrate a real milestone accomplishment. There's not enough of that visible outside the walls of engineering; people still think of it as a boring profession.
A society gets more of what it celebrates. We should keep highlighting the joys of a gigantic plan coming together.