well the thing is, the primarchs were more human personality wise than the chaplains and inquisitors of now-adays. plus the modern people are much much MUCH more aware, and much much MUCH more faithful in the emperor. the reason horus can be swayed is in his deep sadness/anger at emperor leaving and what not, and his brothers because of anything from jealousy to blood-hunger.
mind you, many a chapter (or companies) along with guards, commissars and whatnot still fall to the predation of chaos.
And im hoping by two you mean three
lmao