The issue is that Eich doesn’t appear to think it’s wrong for the state to strip same-sex couples of their equal right to marry. This is clear when you read the blog posts he wrote and how he words this, in addition to the fact that he simply never apologized.

Take his community-and-diversity blog post. He says “So I do not insist that anyone agree with me on a great many things, including political issues, and I refrain from putting my personal beliefs in others’ way in all matters Mozilla, JS, and Web. I hope for the same in return.” Note that he says he won’t force his personal beliefs on others “in all matters Mozilla, JS, and Web”. In other words, he can still force his personal beliefs on others outside of those contexts.

Keep in mind, it’s one thing to think its wrong for same-sex couples to start families but to also live and let live, it another thing to spend money so that the state will enforce that opinion on others.
If he had simply apologized for fueling the state’s stripping of same-sex couples equal right to marry, this would have likely all blown over, . He did everything but take responsibility for that mistake, likely because he thinks stripping same-sex couples of their equal right to marry is desirable.