I'm not surprised that the limerick got changed. The alternative would have been an explanation about why they didn't think a change was necessary. Welcome to a PR minefield there.
Obsidian made the call, the PR drama was averted, this little storm will die out a lot faster than the one after a refusal to change would have. This decision is the politically correct one, and as such the most easily defended. Least harm done to the reputation of the company. In short: it's a business decision.
As for the legitimacy of the complaint: I'm sure that someone was honestly offended. That's a personal thing: what A thinks is hilarious or not worth a second glance can be deeply offensive to B. I may or may not agree with A or with B, but that doesn't make their opinion or feelings any less important than mine. It's anyone's right to file a complaint. It's anyone's right to use social media to draw attention to ones cause. It's Obsidian's right to make a change to their game.
They didn't cave. Pros and cons were weighted and a decision was made. No point in grabbing the torches and pitchforks.
Edit: addition ->
Even though I personally cannot imagine ever being offended by the limerick, I would have done the same: ask the backer if he could write something else. Why? Because if a small change can make others happy, and the writer isn't opposed, the net result is more happy people. That's a win in my book. Now, if Obsidian pressured the writer, that'd be something else. But even though the new text suggests that the writer wasn't completely happy, I'll believe Obsidian when they say that the writer is on board.
I do hope though that – just as I accept that someone may consider this text offensive, even though I don't share their view – they can accept that I may not consider this text offensive, without labeling me anti-transgender, even though they don't share my view.
p.s.: Yes, it could be that the complaint wasn't motivated by being offended. It could be that the reason was trying to draw attention to a cause, no matter what. It could all be some plot or scheme. It could be a self-aggrandising crusade. But there's no evidence for that. So I'll choose to believe in the honesty of people (on the internet, I must be daft *joke*) and chalk this up to a honest complaint. And I think Obsidian handled it in the best way possible.