Two million is indeed a staggering number for such a short amount of time.
The suggestions of infiltration by Nation agents, long-term societal manipulation, coordination of planetside events involving mass gatherings, sabotage of planetary defenses, and well-prepared landing zones for the dropships add up in total to a viable explanation in my eyes. Two million, as in the case at Ostingele, may be a figure that describes their maximum possible haul in a situation where everything went according to the Sansha plan and then some.
Teleportation just doesn't fit EVE tech, and I personally find the above explanations much more chilling than the people Star Trek-style beamed up or even being melted down into DNA. These incursions and mass kidnappings are the kind of operation that would take, say, one hundred years to properly set up... My hope is that we'll eventually come to learn (as players if not IC) that the Nation has been working toward this for a very long time.