They would regard us in the same way the Spanish Conquistadors regarded the natives they encountered in the New World in the 16th Century.
It's ironic that a virus is what killed the Martians in "War of the World."
If anything, the reality would be reversed -- the aliens would infect Earth with a virus deadly to humans. Again, the Conquistador example shows us that smallpox nearly decimated the native population.
I’m coming to the realization that they have always been here. So, does that really make them aliens?
Sounds an awful lot like classical "possession" to me.
Smallpox did more than decimate. Some estimates figure that half the population died. Entire tribes were completely wiped out.
This begs the interesting question of just how did the Spanish regard the Natives after the Conquest. The Counsel of Viadollid held that they were not slaves, but this was largely ignored in practice as the Spanish established economedias, granting the Conquistadores land and the natives on it in order to guide them to Christianity. Unfortunately, those natives quickly became the equivalent of Medieval serfs, and, in my view, this prejudice continues to smother the Mexican economy. More important, however was the notion which persisted into the 18th Century that wealth was a fixed quantity which could not be created, but only shifted from one owner to another. The Industrial Revolution has shown us otherwise, and we see now that wealth is created by expanding an economy, increasing both demand and productivity. A slave system cannot do this, and I would assume that any highly advanced civilization would know that.