So.. First, Dragons are naturally made to dominate and for them adopting a different mindset is much more complicated than us, decisions, all that, their very names describe what they're representing. You'd be blaming anti-infantry weapons for what they're supposed to do?
-Second, Alduin's tyranny was absolute, you ever miraculously changed your mind, you were on your own, there were no other way really and that's clearly discouraging.
-Third, the 'atrocities' was during a War, the Dragon War, you wouldn't expect deaths from that? Does it mean that Ysgramor himself deserved to die for his slaughter toward the elven kind?
-Fourth, imagine the enormous amount of 'atrocities' that would be caused to mankind if Paarthurnax didn't help in overthrowing Alduin AND helping you preventing another disaster.
-Fifth, the meditation, aaaah, regret. For someone named Ambition Tyranny Cruelty to actually stop doing what he was meant to do, it might be wrong for himself too, he doesn't even hide his feelings, being tempted to return to his true self every freaking day, and so far he hasn't done anything bad after the Dragon War which means that he either truly changed, or needed Alduin to be off the map.
-Sixth, the Blades. The Greybeards accepted to embrace some changements as the Dragonborn is an exception to all the rules. The remaining Blades are little more than self-righteous barbarians looking for a revenge, but hey they protect Tamriel, right? So everything they say must be absolute. If you really think that way then you're barely at the level of the dullest of the Thalmor. We're born guilty by default.
To finish, even with all the stuff turning around the Old One, nobody will ever know if one day he'll return to his former self or continue with his promise. But for the moment, he doesn't mind that you slaughter dragons, feast on their souls and make entire bridges and buildings with their bones. I only hope the Dragonborn is a Vampire. For my part I don't mind spending a couple of hundreds of years sitting on a mountain just to check in.