First, it's not a union, it's what the individual employees actually think, and those employees are critical for the company to succeed. Plus, they're not threatening to strike, they're threatening to quit, which could be fatal for Mozilla.
Secondly, while Prop 8 may have passed in California, it's offensive to the Bay Area and Silicon Valley in particular. Santa Clara and San Francisco counties actually sued to overturn it. Even Republicans here aren't suicidal enough to support Prop 8.
Third, how you voted or which party you're registered for is very different from actually financially supporting such an offensive piece of legislation.
It's perfectly acceptable to say you don't want to work for someone who has taken a public political position like this, especially if they backed it up with cash. If it so happens that there are so many like-minded employees willing to do the same that the company is threatened, then it's time to find a different CEO. Though I think Eich could probably resolve this by outright saying he now thinks that Prop 8 was wrong.
In this industry, in this area (I'm an engineer for a tech startup in SF, and I used to line in San Jose) supporting Prop 8 is as far to the right as banning birth control would be in the rest of the country.
I don't know what it's like at Mozilla, but I know the CEO of my company. Everyone knows everyone here. If a Prop 8 supporter suddenly became the CEO of my company, I'd likely turn in my resignation the same day. I really doubt I'd be the only one either.