The problem is who's deciding what is and isn't acceptable, RMS has been saying clearly derogatory statements about religion, the basis of most of our shared morality, for decades without a single peep from the virtue crowd. He says a few edgy this about something else and then the pitch forks are out.
The problem is that I'm not sure we have much of a shared morality any more.
Software development forces us to be more precise about what our process is. Sales wants to automate their pipeline - oh but what do you mean I have to tell you who to call next? Just call the important ones. We can no longer 'fudge' things.
Agile methodology is causing this problem in many companies. Asking senior management to stack rank their projects is an intensly political issue. Saying the project timelines will vary based on team velocity takes away simplicity of project management.
As software eats the world then more of the world must be upfront and precise about what it means. This is going to lead to a lot of soul searching. The most obvious example is the Trolley problem in autonomous cars - do you program a car to swerve to avoid the child, killing the driver, or save the driver, kill the kid.
This sort of devils own choice will become more rampant as more of the world becomes automatable.
Online speech is just one of these. Now that every pub conversation can be spread to millions of listeners, we need to find ways to agree on what is and is not acceptable.
The problem people are finding is that what was tolerated by people in the 19th hole in Alabama is not acceptable by people listening in Delhi.
The human species is going to have to find ways to get along together. I think that will (eventually) be a good thing.
And now it's unfortunately nearly impossible for us to have a discussion about what various religions did or did not say about topics like homosexuality.
People all around the world have state sanctioned freedom of speech but are oppressed by the majority in their country.
This infantile view of freedom of speech is simply a way to pretend you care about freedom of speech while sanctioning other ways to silence/punish people. Even when that punishment is completely disproportionate too.
So, whilst I was thinking of some old white guy from the UK I saw last night complaining about 'cry-baby safe spaces', and felt that I could happily not listen and judge him, you are more sensibly thinking of ... a gay rape crisis centre that wants to publicise and support victims, but they find themselves in Russia or Turkey.
So its not enough to have freedom of speech, one also needs freedom from persecution and the other rights listed below:
I'm not sure how you can solve the "problem" you describe.
Freedom of speech means just that - you are free to say what you want/think.
Others don't have to agree with you. They might leave the room/not be your friend/unfollow you/fire you/stop buying your products.
If your opinion is against the majority in any situation, you're going to have a hard time - whether it's about something important, or just whether you think pineapple should go on a pizza.
The problem is that I'm not sure we have much of a shared morality any more.