Another is the saying "tolerance isn't a virtue, it's a peace treaty", which I think really cuts through the apparent dilemma you highlight.
Sometimes, policies that follow from abstract ideas do harm to some people, in the interests of helping others (hopefully more), or do harm in the short term, in the interests of helping in the long term. Sometimes, these tradeoffs are good to make; other times, they are not.
There is no hard and fast Golden Rule that can serve as your bedrock if you treat it as something to be applied in all situations without critical analysis. The closest I can come is "care about people", but even that requires careful application, because there are situations when you must do things that hurt some people—even people you do care about—in order to do what is best for all.
It is an example of the paradox of tolerance: If a group believes in tolerance, absolutely, to the point that they tolerate intolerance, then over time, those who are intolerant will tend to gain power within the group and the tolerance will be eroded (except, of course, the tolerance of those intolerant beliefs that usurp them).
Absolutism of any kind is generally going to lead to problems in our imperfect, non-absolute world. Free speech maximalism is just one example of that. If we put people and their genuine needs before abstract principles, that will tend to be a better guide for how to make a society that serves everyone—and, indeed, allows the greatest freedom for the greatest number.