Yes, Hally's relationship with Sam would have impacted his life regardless of Apartheid laws or his relationship with his father. The fact is that Hally formed a stronger bond with Sam than he had ever forged with his father. Sam was in a sense the father Hally had never had, in addition to being both friend and employer.
Hally doesn't get along well with his father, and the conflict between them is what opens the door for Sam to become his father figure; Sam encourages Hally to do well in school and to study and Hally responds. We see this response throughout the novel, and as the author unveils the depths of their relationship through flashbacks we can see exactly what Sam meant to Hally at different periods in his life. They played chess, flew kites, and played games. Hally escaped from unhappiness in Sam and Willie's room. Later, that bond would create a lasting friendship.