Michael's policy was that no traitor or enemy got a pass--ever. Fredo was an eventual dead man from the moment at the Superman show when Michael realized that Fredo betrayed him to Roth. The bit in the car in Havana ("You're still my brother, Fredo!") and his instruction to Tom when he got back to Nevada ("Tell him I understand that Roth misled him...") were both designed to lure Fredo back and keep Fredo alive until he could pump Fredo for more info--and to await Mama's passing so he could finally whack Fredo.
In sum: Michael didn't change his mind about Fredo--he was waiting for the opportune time to kill him.