EA doesn't come out looking good. Their defense is almost as idiotic and ignorant as the letter writers' attack: "Every one of EA's games includes ESRB content descriptors so it's hard to believe anyone is surprised by the content. This isn't about protecting children, it's about political harassment."
Why in the world should the possibility of a gay relationship be included in "content descriptors." It's an a priori claim that gay relationships are objectionable (or potentially so) and thus require content advisory warnings. So, no, EA doesn't come out of this looking good. They come out looking like asswipes whose only good quality is that they know how to speak legalese better than this letter writing group. Imagine if there was a warning label on a game that said "Rated M for potentially objectionable interracial relationships." Ignorance is ignorance.
Make no mistake, both EA and these letter writers are attacking gay rights. One is just more subtle about it.