Rather than respond to everyone individually, I figured I'd just post one singular response here, so it didn't get lost in the comments.
I got alot of responses saying that it was heavily implied that the reason for Rose's baby and her muteness was because when the military invaded Liore, she stood up to them, and she was raped.
I honestly had the same theory, because it's the only one that even remotely makes sense..... HOWEVER.... If it was implied in the anime, it was very vague, at best.
I was curious because people were saying it was obvious, so I dug out the episode summaries to find out which episode it was, and to my knowledge the last reference to Rose is in Episode 14 where it shows the military taking over Liore and bullying her while she's hiding out with a bunch of kids. So I dug out the DVDs a little while ago, went to episode 14, and sat through all the crap about Marcoh and the Philosopher's Stone and Scar, watching the parts with Rose and Liore very carefully for this "heavily implied rape scene". It wasn't there.
The closest you get is this:
Rose is hiding out in a house with a bunch of kids because the military is taking over Liore. The military busts into the house and asks her to give them information. (the only slightly questionable part about this is that the guy grabs her face by the chin to try to get her to talk, but that doesn't mean rape to me, just an interrogative tactic to scare her) Rose refuses, the guy slaps her, and Rose quotes Ed's line about them having their own legs and standing on them--or something to that effect anyway--and then the episode ends.
I watched this with two other friends, and neither of them thought that it meant "heavily implied rape". One of my friends even made the point that the scene was so minimal that by the time you see Rose again around Episode 40ish, you don't even really remember much of it except the Ed-quoting. I suppose that, when you get to Episodde Forty-Whatever when she shows up, and you see the baby, the initial "WTF" of it all would cause you to look back toward that scene, and think into it alot. Because really, the only explanation is that she refused to give information and got raped and tortured because of it. However, it's never actually stated that this happened, nor does the actual scene itself really imply it at the time of watching it.
So, right now I'm going to think of this theory in two ways:
1] People are thinking rather far into it in order to explain why there's a baby there and she's mute.
2] The production team made it ambiguous purposely, so that people would think so far into it and come to the conclusion that she was raped, in order to cover up their plothole.
I originally asked if there was an official reason, or an agreed-on-by-fans explanation for it. Either way, I got my answer as to what people thought, but considering Episode 14's vague approach and the fact that I haven't seen anything on official sites supporting it, I'm going to accept this explanation as the latter classification, rather than the former. I'm not disputing it with anyone, or saying that I don't believe them, because really it's the only understandable reason for it, but.... I don't know, re-watching Episode 14 just made me question things more. u_u;;;
Thank you, everyone, for your insight and opinions!