When we talk about "intolerance of intolerance" being OK, we're being a bit flip. What is actually meant by the phrase is that it's OK to make people act tolerant, even if they aren't naturally inclined to do so, in order to preserve a particular group's rights. They can hold whatever opinions they want, but they have to be civil. But Eich was already doing that. He was even one of the people who helped draft Mozilla's inclusiveness guidelines. This was just punishment because Eich held a particular opinion, not because he was actually having trouble tolerating gays in the organization.