"The pilot definitely definitely pushed the distress call, which raises a red alert, and means the incident was referred to the Indonesian airforce. There's another button that can deactivate it and now we're asking why the pilot didn't do that.
Once you activate a hijack response there is no turning back as how do the authorities REALLY know if it is over or not.
You could activate the transponder only to be overpowered and a hijacker deactivate it.
If someone is trying to knock down the door you arrest them and let the police sort it out. If he goes free no charges laid so be it. Just because you get arrested doesn't mean you're guilty.
He's damn lucky there wasn't an Air Marshall onboard.