I just wish I could figure out if she is trying to be protective when strange people/dogs come around or if she is nervous and we should be concerned about the beginning of aggression.
She's trying to be protective of HERSELF. She's not trying to protect YOU... in fact, you thinks you should be the one to protect her, and she's trying to tell you when things scare her. It's a phase a lot of GSDs go through around adolescence. You're right to be concerned, but don't freak out worrying about "aggression", because that will make it worse. The treatment for this is to socialize with friendly strangers (classes are great for this) and project confidence, so that she can learn that things aren't so scary.
It just seems strange to me that she is acting like this since we've been away - but now that's she back home the behavior is continuing. I hope that something didn't spook her. She has been a little disconnected from us since we got home. We have to re-bond a little.
It's possible that she got "spooked", but it's just as possible that she's entering a behavioral phase common to GSDs. Where she may have been shy and retiring with strangers before, she is becoming more defensive now because her defensive drive is awakening.
I don't know how much has to do with you being away, since the nervousness is a temperament trait that is at least partially genetic, but it's possible she missed out on a prime socialization window while you were gone.
Re-bonding will be a great thing. Training, playing ball, going for walks, all the good doggie stuff will certainly help her get through this. Another obedience class, maybe intermediate obedience or something like that, will help with the bonding process. It will teach her to look to you for cues when something a little bit scary is going on, so that you can be reassuring to her without rewarding fearful behaviors.