I would submit it is logical - albeit logic serving an outcome we find deeply disturbing and incomprehensible.
If it wasn't for the satellite pings (a detail perhaps not known about or somehow overlooked), we likely would have no idea what happened. But strip away the satellite stuff, and everything else fits with a desire to disappear without trace.
Why? Who knows. But history is full of people who chose to disappear.
Who has been harmed by this? That provides best guess at motive. Well the Malaysian government has been horribly exposed on the world stage. It has generated ill feeling between Malaysia and China (not what he Malaysian government would want).
I am not suggesting it was a particular pilot who supported the opposition. We can't conclude that. But someone (could have been other than pilot) who wanted to damage Malaysia for some reason.