"Free speech has nothing to do with this, this is someone whose actions many people found incompatible with what they saw as Mozilla's values, both inside and outside of the organization, and who can blame them?"

I can blame them. Mozilla makes a web browser. Gay marriage has nothing to do with Mozilla's mission or with the political issues Mozilla has to deal with as part of its mission. I could understand the uproar if Eich had donated to a "ban free software" cause, but that is not what happened.

You're right, this is not about free speech. Eich was not punished for what he said, he was punished for what he thought. The donation is irrelevant here, other than the fact that it revealed Eich's beliefs. There would be just as much anger and vitriol if instead of a donation someone revealed that Eich had voted in favor of proposition 8.