They may not have known humans were there, but they knew the Alterrans/Ancients were. Plagues are the Orii MO, and we know they and the pre-ascended Ancients were fighting at one point. I'm pretty sure what happened is: plague wipes out most of the population of the Milky Way, Ancients reseed using the device at Dakara, this time shielding themselves from the Ori so that the Ori don't think there's anything worth bothering about in this galaxy.