Something that was acceptable 8 or so years ago became unacceptable and was used to retaliate against him
No. The people who consider it unacceptable now considered it unacceptable then. They just didn't know about it then.
Nothing was used against him. People decided they did not want to work for or do business with someone whose beliefs they find distasteful. They have that right. He was not fired--the board knew about his beliefs and hired him anyway. He chose to resign because he would have been unable to run the organization anyway--because so many people refused to work with him. Again, they have that right. Suggesting they don't is to suggest that his free speech trumps their right of free association.
To use the good ol' reductio ad absurdum, if I found out tomorrow that my boss was making sizeable donations to the Klan, I would in fact start looking for new employment too. I don't want to associate with someone like that, and I don't want someone like that in the position of recommending or not recommending me in the future.
In other words, shunning is a perfectly legitimate response to bigotry. Which is all that happened in this case.