The fact that you would consider your counterfactual a mirror image is itself problematic.
In the case of the Foundation, it supports exactly what it purports to support. They’re like the EFF and other civil rights organizations. If you consider the EFF left wing, I think that says a bit more about where you stand.
The original article was outrage-bate blog spam, with random Capitalized Words and the prolific use of “scare quotes.” It doesn’t even say anything. No charges of misinformation. No citation of law. Just “They have a Billion Dollars!!” kinds of sentences.
On the other hand, the CEO of a company - particularly a small company - lends his personality to the company. It often makes sense to co-identify them, given that the CEO has an incredible amount of influence.
So if you are saying that libertarian software project : libertarian institutions :: conservative ideas : homophobic legislation, I guess you’re just really endorsing the position of judging the company by the politicians and politics it supports. If you see prop 8 as being as fundamental to the conservative position as internet freedom is to an organization specifically dedicated to preserving internet freedom, all I can say is that I hope more people start to see it that way.