Well, there's actually enough lore in the game to contradict the official propaganda. It seems Parthanaax's rebellion against Alduin weren't necessarily for altruistic reasons, and Odahving's mentioning their willingness to challenge Alduin at the first sign of weakness was insightful. Recalling that Alduin had HIS mortal followers, it doesn't take a stretch to imagine Parthanaax had them as well, and then the official story of what really happened got changed over the centuries. Parthanaax's insertion as the leader of the Greybeards could be looked upon as a clever move. Empire and dragons living side by side? I know that Tiber Septim promised protection in return for the dragons' service, but it turns out that might not have happened, either.
I am aware that Alduin that has followers for himself, (which I take it they are Dragon Priest, whom are like the highest ladder in politic until they are overthrown after the war, whom I would assume already screw their human brothers and sister that they rule over), but it cannot be deny that during that time, crap happens and pretty much a LOT of humans living Alduin's wing are like "Screw this, we're rebelling!" Their hatred allow them to make dragonrend and we saw the final via Elder Scroll how much hate and desperation the warrior fought Alduin at the last battle. As for Greybeard part, I would doubt that its a clever move on Parthanaax "clever move" and more so on him helping himself not being like his older brother. Meditating and keeping his mind clear.
Oh and well, the dragon did serve the Empire. One was send to Hammerfell (by the Empire as a last mean of winning and owning that Province) and pretty much a breath fire on the leader's warship and won the battle. The dragon, http://www.imperial-library.info/content/recovering-soulgem, even claim himself to be Tiber Septim's proud Soldier. There was also one that was station in a space station call http://www.uesp.net/wiki/Battlespire:Starlover%27s_Log and that dragon and nearly 90%-99% of the people station there died in the daedric invasion. They also make great living decorations, as said in the http://www.imperial-library.info/content/pocket-guide-empire-first-edition-cyrodiil.
I have real issues with the plot, btw. All I can say that's Parthy's pointing the PC the way to learning about the shout can be partly explained by a desire for self-preservation - he faces a reckoning from Alduin, after all. However, I really wish Bethesda had implemented MQ differently - choosing sides should have happened much sooner, and there should have been an alternate way to learning about the Elder Scroll. As is, they took the Bioware route of faction idiocy.
I would like a choice to actually convince the last two
"Blades" to just let Parthanaax live and actually focus their duty of the Blade and not living off their fantasy of being dragonkillers.