Great men are above the common principles of morality.

Such principles do not reach to the pedestal of a great man.

Did Shivaji commit a sin in killing Afzul Khan?
The answer to this question can be found in the Mahabharata itself.

The Divine Krishna teaching in the Gita tells us we may kill even our teachers and our kinsmen, and no blame attaches if we are not actuated by selfish desires.

Shivaji did nothing from a desire to fill his own belly.