Except we did not collapse due to the Spanish Flu, which if you believe the Vilani did, it is contrary to the historical evidence, and that is the stretch you are believing in.
Who said the Vilani collapsed due to the Terran plagues? Someone suggested that if a pathogen was deliberately introduced to a population prior to an invasion, the result could be that the defenses were weakened or disrupted. This has nothing to do with the canonical history which says that the plauges were carried along by the Terrans when they invaded the Vilani worlds, entire armies composed of Typhoid Marys.
I can't remember if the two pieces DGP wrote about the Plague of Duskir were authorial voice or viewpoint writing. Either way it has been suggested that those two passages should be viewed as what "everybody knows" in the Classic Era rather than the exact truth. I'm pretty sure IW takes that approach. In the Classic Era "everybody knows" that the Terrans took over Vilani worlds because the plagues killed off entire populations. When we discussed it while playtesting Rim of Fire and IW, we decided that what actually caused replacement of Vilani with Terrans was different reproductive strategies, with Terrans tending to having more kids at an earlier time of life than Vilani.
Certainly IW never mentions anything about Vilani societies collapsing or Vilani populations being drastically reduced.
Hans