Since MCAS and autopilot are two different things and MCAS is only active when autopilot is off I think it is faulty to assume that something that disables autopilot would disable MCAS--but in the heat of the moment I can see room for confusion.
The point in that the Lion Air pilots had no way to know of the very existence of MCAS, and therefore thought that the autopilot is the only system on the plane capable of issuing intentional trim changes, and therefore that disabling it would stop them.
