Since the pilot asked for a change in flightpath can it be assumed that the pilot didn't realize the danger the TS posed?
Nothing can be assumed. And we don't know the TS posed any real danger. (Although it probably will turn out to be related, we don't
know that yet). It likely was a routine request for deviating left (west) around the cell being painted. Happens all the time, everywhere.
I agree with the fact that the PIC has the right to make decisions in order to save the aircraft but the PM needs to notify the atc before the decision is carried out or in adequate time. Otherwise their could be risk to other nearby planes.
Of course, but it doesn't always work that way. If ATC won't/can't give you what you need when you need it, execute your plan, advise ATC/declare an emergency, then seek forgiveness, preferably once you're on the ground, safe and sound, with your hand wrapped around an adult beverage.
If you crash, the controller likely will feel really bad. You won't feel a thing.