One must keep in mind that Fredo's impending murder is in Michael's mind at this time. He cannot listen to reason about Roth, because he cannot murder his brother but let Roth survive.
One has nothing to do with the other.
Whatever his personal feelings about Fredo's fate, that decision had been made. He was now dealing with somebody else.
Roth had done immense damage and had intended to do even more. Michael would've wanted his plane met no matter what his physical condition was.
