How does St. Clare’s father justify permitting Mr. Stubbs to occasionally be cruel to his slaves?

He doesn't justify Stubbs' cruelty, but rather admits that unless he allows Stubbs his "cruel" moments, he'll lose him as an employee.

"I used sometimes to hear my mother reasoning cases with him, -- endeavoring to excite his sympathies. He would listen to the most pathetic appeals with the most discouraging politeness and equanimity. 'It all resolves itself into this,' he would say; 'must I part with Stubbs, or keep him? Stubbs is the soul of punctuality, honesty, and efficiency, -- a thorough business hand, and as humane as the general run. We can't have perfection; and if I keep him, I must sustain his administration as a whole, even if there are, now and then, things that are exceptionable. All government includes some necessary hardness. General rules will bear hard on particular cases.'