He's not bad. It's Cato's situation again. He just a man with a beliefs of what's best for the country.
While Cato is not too plot deep enough of a character Howley had written, Adastra as a whole are a mirror of Rome's real life history. And that Cato are based on Cato The Younger, which is an old-time with a beliefs in what he done is best for the country, the beliefs he was taught upon growing up.
Gunner done all of that bad stuff dues to what The Observe had poisoned his mind with, not with sweet words, but trauma. It implied that The Observer had tortured Gunner through future vision over and over again, living through the many death and watching his kingdom crumbles. He should've hate Alon for being so incompetent, but he didn't. He still love the kid and do not fault Alon for it. (He'd chopped the observer head without hesitation the moment there were an indication that Alon was hurt. His emotional side in heat of moment and not logically driven.)