I think the whole May thing is being blown out of proportion. She has to be reporting to Fury since the whole 'Coulson knows' thing came immediately after the mission to the Guest House. This can only be a reference to the fact that Coulson now knows where the resurrection serum comes from. The Clairvoyant can't be reported to since he doesn't know anything about the serum, nor can any lower agent be in the loop since Fury code locked the file to His Eyes Only.
Also, the Bus may not be remote accessible for flight path alteration. May, Coulson, Skye and Fitz are in the cargo area of the plane when all of a sudden it turns and heads for Hand's location. The one conveniently absent is Ward who just executed Nash for really no good reason. Ward is a trained field agent, he wouldn't be that emotional. His immediate execution and really weak reasoning for why he did it makes it easy to suspect him of being a traitor. Plus his mission also had what was most likely a maximum security super-max prison where the guard room was empty. There is no conceivable reason for that to occur. If there was an emergency that required the guards to vacate that room then alarms would be blaring loud and clear.