There's no doubt that Roth took Moe Green's murder personally. But I think the "nothing to do with business" rap was a clever tactical move on Roth's part:

He and Michael were at the nub end of their duel, and probably knew that the other figured out their motivations. Michael knew that only the promise of the $2 million was keeping him alive in Havana, and Roth knew that he'd have to move against Michael, with or without the money, before dawn on New Year's Day. Roth saw Michael's reluctance about the money and was steadily pushing him into a corner, almost implying he was cowardly because he had doubts about the rebels. He reduced Michael to saying, "Uh, I just wanna wait..." Michael looked weak, and he knew he couldn't forever stall Roth.

So, I see Michael's indignant, "Who had Frank Pentangeli killed" snarl as an attempt on his part to regain the "moral high ground"--push back at Roth by adding Pentangeli's killing to the reasons he wasn't coming across with the $2 million. And Roth, sensing it, brilliantly put Michael in his place with the "...nothing to do with business" rap. He'd regained the "fatherly high ground."

However much Roth "loved and trusted" Green, he could not justify risking his own life or reputation to defend Moe, who, after all, was losing money in a business that was engineered to make money hand over fist. He might have recognized that Moe's boast, "I tawk to Barzini...I can make a deal with him and still keep my hotel," would represent a mortal and overriding threat to Michael. And Roth was in no position to thwart Michael's ambition to become Numero Uno in Nevada--except by killing Michael. That was business. From his viewpoint, it'd be better to have Michael pushing at him in Nevada than Barzini for two reasons. First, he had a sentimental family connection with Michael through his long association with Vito that he thought he could play to his advantage. Second, he saw Michael's lust for "legitimacy" as an Achilles' heel that he could use to keep stringing him along until an opportunity presented itself to kill Michael. Neither applied to Barzini. So, Michael was the lesser of two evils--or so he thought.