Just trying to get some other people's thought on this, because it has me rather confused.
Emily was defeated after her transformation after the wraith battle, and she began to run out of the keep. She had mentioned bringing the Magicant piece to the Angelo. (Making me wonder if she was always on that side.) Her likeness (and name) then reappears in a later segment with her facing off against Handsome Jack right before Yo-Lee appears, just to be defeated again. Was this the same Emily? Did she get resurrected? This just left me very confused, although I may have missed something that could have revealed the truth.
Emily had a symbiote, like the ones in the labs and the one Angelo has. She was not aware that she had one, in all likelyhood, and while she was not evil, the symbiote was. That was why she didn't read as evil to Jordie's Detect Evil spell. Marvin confirmed that the symbiote was a separate person from her, as when it took her over, he became able to attack it despite the spell.
Now, going further back, Emily was likely created in the lab, and was at least partially brought up under Souballo Empire beliefs, due to her referring to elves the same way SE soldiers do. Since making life is rather difficult, once the first Emily survived a certain period, they started making clones of her, as it's easier to mass-produce then to come up with something original. The other Emily we saw was raised by the SE, and used as just a soldier, instead of whatever the original Emily was meant for (probably intel gathering or sabotage).