My own notion for the Coulson controversy would be: Coulson comes back with no explanation. Everyone is confused, but knows better than to inquire too far into Fury's machinations if it's above their pay grade.
Then eventually it's revealed that Coulson is really a Life Model Decoy, and is treated basically as a disposable agent. Perhaps Coulson is the first prototype LMD, patterned after one of SHIELD's most successful agents. "Coulson" dies (is destroyed) repeatedly, as a kind of grim mockery of the real man who died on the helicarrier.
How do we know the guy on the helicarrier wasn't an LMD?