I believe that Michael was 95% certain that Roth was the perp when he called on Frankie. The emotional outburst, I think, was a test to see Frankie's reaction. But the real test was, "Settle these problems with the Rosatos." Had Frankie declined, Michael would have been suspicious.
I don't know if he would have suspected that Pentangeli had, as he would put it in a later movie, "the wit" to pull off a hit on him. Frankie is in fact still reluctant to "settle these problems with the Rosatos," and doesn't agree to it until he confesses to Michael that he lacks the intelligence to make "big deals" and until Michael has to draw pictures practically to demonstrate how this ruse will make Roth feel comfortable.
