Why would Varys consider Kevan a good man considering he was the loyal underling of a cruel tyrant like Tywin?

Let’s examine the scene:

“Ser Kevan. Forgive me if you can. I bear you no ill will. This was not done from malice. It was for the realm. For the children…This pains me, my lord. You do not deserve to die alone on such a cold dark night. There are many like you, good men in service to bad causes…but you were threatening to undo all the queen’s good work, to reconcile Highgarden and Casterly Rock, bind the Faith to your little king, unite the Seven Kingdoms under Tommen’s rule.” 

As I’ve said before, Varys is an arch-utilitarian who doesn’t blink at the idea of building Utopia by spilling an ocean of blood and raising up a mountain of skulls. Hell, this is a man who mutilates children so that they can’t betray his secrets, who does it “for the children” – and he’s not insane or lying, he’s weighed the short-term costs in human lives versus the long-term gains of a complete remaking of the social order by enlightened despot. (Incidentally, this is why utilitarian revolutionaries are so dangerous, because their faith in the future justifies any atrocity.)

So how would someone like that look at Kevan? 

I don’t think Varys would object to Tywin’s methods as much as his goals and his frame of reference – Tywin was fighting for the glory of House Lannister rather than for the greater good; his efforts to keep the Seven Kingdoms together with war and war crimes would have been undone by Joffrey’s unstable tyranny or Tommen’s well-intentioned weakness or Cersei’s paranoia and misgovernment; and none of these people have the very precise training and worldview that would allow them to be a “perfect prince” who could make systemic change. Hence the “bad cause.”

At the same time, when Kevan took control, he didn’t act for his own benefit but to strengthen the crown and restore order in the capitol – by rebuilding the alliance between House Lannister and House Tyrell that gave the regime its political constituency and military hegemony, by ending the clash between Faith and Throne that was dividing the body politic and threatening further uprisings. Varys sees that as the actions of a “good man,” one who looks out “for the realm.”