What about the freedom to have personal beliefs, and do what you want with your own money and time?
If anything the people criticizing Brendan Eich are trying to take away his freedom...
Freedom of speech isn't freedom from criticism, and criticism isn't censorship. Freedom of speech isn't freedom from social consequences for speech. Freedom of speech isn't an unconditional guarantee of employment.
Sometimes, freedom of speech becomes distasteful. I don't feel like this is one of those times, but I can understand why someone might disagree. In this situation, I see one person exercising their freedom of speech (in the form of a campaign donation) and a group of people responding with their own speech. That seems fine to me; if you disagree, could you elaborate on why, or describe what you think these employees should do instead? It seems to me that people responding to Brendan Eich should not have less freedom of speech than him.