There's certainly more information to be had about the Emperor's designs, but I think there's enough out there to indicate that the Traitor Primarchs were at best misguided and at worst outright evil.
The Emperor's grand scheme centered on bringing Humanity under a single power while simultaneously suppressing the fundamental truth behind the workings of the universe. He absolutely needed to deny Chaos its greatest psychic fodder, and the "moral imperative" of protecting Humanity from the predations of the Warp (given the precedent of the Age of Strife) justified (in his eyes) the means by which he would do so. Those means, of course, included total war, the extinguishing of entire planets, and a totalitarian rule that on the one hand created vast and wondrous works... and on the other brutally suppressed freedom.
Ultimately, one must remember this. However flawed the Emperor, however brutal in his drive to save Mankind, the Ruinous Powers are even worse. Lorgar can in no way justify his schemes and actions following the rebuke he received from the Emperor. Rebellion? Sure. A ploy to brainwash, corrupt, and/or blackmail his fellow Primarchs into falling in line with gods with no love for Man? No excuse.