(possible Rebirth spoilers)
I've seen a couple of cutscenes from Rebirth and there's one where a doctor tells Tifa that a Shinra helicopter saved her and that they "aren't all bad". Plus they seem to be setting up that there is a more "Tankie" version of Avalanche in Wutai that might be bad?
Shinra Mayor is a traitor that helps Avalanche get up the tower too in the first Shinra section of the game.