Not necessarily, because we don't actually know why the dragons are here... we don't know the story. For all we know the dragons could come back as benevolent creatures, but humans and elves could be so distraught by the Nordic interpretation of the god (Fred? Lmao) that they could wage war against the dragons, regardless of the dragons' intent. Maybe imperials are right, and its akatosh coming to cleanse the world of a greater evil, and humans are just blind to the truth. Or maybe humans are that evil. It all depends on perspective at this point. We don't know how the dragons are ultimately going to play into the story.
Its probably more likely that both are right.
There are theories that in some fiction sets, gods are what people believe them to be, which would fit well in TES.
For instance, Akatosh and Alduin represent the same thing, but could be different aspects of it, like different personalities, each with its own goal.
And even if it doesn't follow that, there is a grain of truth to each story. Im sure Akatosh/Alduin/Fred has done both good and bad. The Imperials over-look the bad, or attribute it to something else, where as the Nords over-look the good or falsely attribute something else. Its more likely that our god Fred has his/her/Fred's own goals in mind, not any mortals. Maybe Fred's goals was in line with aiding mortals, until now where they are in the way?
Either way you end up with a similar point of, were not quite sure whats going down.
Although I believe that in this instance the Nordic interpretation of Fred, aka Alduin, is more appropriate. Even if not i'll find a way to kill him.
"Alduin, meet Wabajack!"
Sheogorath beats all...