I am sure there are a number of folks complaining about Star Wars Rebels season 3 and it’s portrayal of Grand Admiral Thrawn, but let’s face it, he was not all flowers and sunshine in the books.
The first time we meet him, he has no problem sacrificing a couple of patrol ships in order to determine the nature of the opposing commander.
He had a man executed in the middle of the bridge of the Chimera just to show he didn’t tolerate incompetence and not accepting the blame.
He certainly knew the truth about the situation on the Nogri homeworld, and let it continue because they were too useful to him.
He was fine with ordering the kidnapping of a pair of infants to keep a mad Jedi occupied. Even if he had no intention of letting Joorus keep them and train them, they were still being targeted for abduction.
Thrawn is one of my favorite villains, but he was always a villain. Even at his nicest, he was quite willing to take ruthless measures to ensure his vision of order in the galaxy was fulfilled. Unlike The Emperor or Vader, or any number of Imperials, he didn’t do it out of anger or pettiness, but pragmatality. Which makes him scarier.
So, yes, I can see him killing factory workers whom he was suspecting of sabotaging the Imperial war machine. Their example would make others less inclined to follow suit.
Thrawn was never intended to be a good guy, by either Zahn, or the current Rebels writing team. He was meant as a scarily competent antagonist to challenge the heroes.