Yes they did. There is more to communication than the specific words used. Tone, timing, delivery, emphasis, etc all are part of the message. If Facebook altered any of these to be different from the expectations of the user without informing them beforehand then they changed what people said. There is MUCH more to human communication than the syntax used.
I'm not sure how you think they changed the tone, timing, delivery, or emphasis of the messages. Apparently they used real posts and posted the entire content of each post without alteration. From what I understand, though I'm interpreting from a few different stories that I read, all they did was to alter the algorithm that Facebook already uses to choose which posts to show in your feed. They didn't insert or remove words from the posts. They didn't do anything to really re-contextualize them.
Whether people realize it or not, Facebook already filters and resorts your feed to emphasize posts that they think you're interested in. If you pay attention, you'll notice that when you have a friend that you "Like" a lot of their posts, then more of their posts will show up in your feed, and they'll appear higher up. I suspect that they also do things like prioritize posts with links from friends who you follow their links. I think they probably even do things like, if you've looked at a persons' profile a lot, or perhaps even if they look at yours a lot, the posts will be more likely to show up. I doubt that Facebook has made this algorithm clear, but it's clear that they're doing things like this.
So it seems that all they did was to add into the algorithm for some users to favor posts with happy words, and for other users posts with unhappy words. I don't think they're altering anything about the tone or emphasis of any individual message. I don't say this to really defend them.