There were two fan ideas I remember reading. One was basically the Primarch wasn't willing to go along with all the wanton human slaughter, willing to play live-and-let-live with totally self seficiant human colonies that don't want anything to do with the Imperium. Meh.
The second was that the Geneseed quirk made the Primarch and all his Marines into soulless Pariahs. And Lorgar, Magnus and the others simply thought there were abominations. And that's actually kinda' interesting.