A pilot is expected to follow procedure when that's called for but ultimately has full responsibility and can make any call they want. Procedure is never going to cover the range of scenarios you can run against and there's no time to reach out to the chain of command when something goes wrong.

Ejecting could save you but send the plane crashing into a city, and that's just one of many scenarios.

If he was flying with instruments in bad weather and felt that he could not trust those instruments that seems like a good reason to eject since you can easily end up in the ground or a mountain. I don't know if switching modes like he did was standard procedure and if the resulting failure was unusual or not. Maybe he wasn't familiar enough with the airplane's systems. That said, there was a real failure that seems to have happened at the worst possible times.

At the end of the day, the bar is set really high for someone in this position.