This reasoning is bending over backwards a little too far. If the goal was to have marriage equality, then supporting a ban on marriage equality is not going to achieve that. Working against the ban would be much more likely to lead to marriage equality, because the supreme court can always decide over the
next marriage equality ban that pops up. Secondly, the supreme court
does take public support into account in its decision. Thirdly, the longer the wait, the more support is shifting in favor of marriage equality. Fourthly, he has not said anything to deny that he is against marriage equality. Do you
really believe that there is a non negligible chance that he is secretly supporting it?
Your comparison between not choosing to work at a company and refusing to hire somebody is invalid. It is perfectly okay for Brendan Eich to choose not to work for a company with a gay CEO. Not hiring somebody is a completely different matter. The next thing is that Brandan Eich is not some random guy at Mozilla. As the CTO he has a lot of power, and influence over company culture. If you are gay (and also if you aren't) then it's entirely reasonable to take this into consideration, since this might cause you a lot of grief. For example, perhaps it would be wise to ask gay people who are working at Mozilla for their experience. Also, your good work at Mozilla would be increasing the influence and/or wealth of the CTO, which would be partially going to these these causes. It all depends on how much this will influence you within the company. Will there be lots of gay jokes? Will it be taken into consideration later in whether to fire you or not? These things are hard to find out, and there are plenty of companies that are a safe bet in this respect.
To be perfectly clear, I also think it would be wrong to fire anybody for being for prop 8, just like it's wrong to fire somebody for being against prop 8 (as long as the political beliefs stay outside the workplace).