I know several people who were involved in bringing this topic to XSEED's attention the week the game released. Originally, while the person running the XSEED Twitter was a little defensive (and understandably so), they ended the relatively calm discussion by saying they would consider this stuff more in the future. It seemed all was well until some people got wind of it, cried censorship and sparked the debate again not even a full day later. Worst of all, whoever was running the XSEED account that weekend (the same person I assume made that forum post) decided to use it as their own personal soapbox instead of responding professionally to more concerns regarding the lines (yes, LINES, not just one line) in the game. This escalated things and made the entire company look bad as a result. "It's satire, like South Park!" was a common defense from the XSEED account, which is a silly way of saying, "We can do what we want because we're claiming it's satire" instead of, I don't know, taking the concerns of loyal fans into consideration like they said they would. As you might expect, this pissed even more people off. Crazy, right?
In short, it's less about changing the lines and more about respecting the wishes of loyal fans who bought the game DAY ONE and wanted to express their concerns over a few lines they saw as offensive. They didn't approach XSEED with any malicious intent. It all began as a respectful discussion and everything seemed like it was going okay. Now, with the follow-up tweets and this forum post, it seems like "taking fans concerns into consideration" means jackshit. Sorry, loyal customers!
Also, one last thing, I guarantee if those lines were altered slightly, very few people would notice or care. They don't matter much in terms of the overall narrative of the game, simply optional conversations you can view at anytime. And no, the people who took issue with them couldn't just "ignore" it because they didn't know they were in the game to begin with. This wasn't really an issue until much after the game's release.
tl;dr - Whoever ran the XSEED account and made that forum post is kind of an asshat and made the entire company look bad as a result.