The road to Hell is paved with good intentions.
He probably believed the actions he was taking was the best for the Federation.
The premise is a flawed one, though. Marcus could have absolutely taken Kirk's surrender offer instead of going right to Evil Villainy "I was never gonna spare your crew!" Well it's nice to know that you didn't seek any way to avoid destroying one of the most powerful and advanced ships in your fleet, along with it's entire crew. Very forward thinking for your war effort, Marcus!
I really do wish Marcus had been given more dimension. Weller is a great actor, and what he was given he took as far as he could. Had the character been given more scenes with his daughter, or at the very least been given more of a chance to lay out why he was doing what he was doing, I think it would have benefitted the dimension and truly been the "Good man making the bad choices." That he was supposed to be. I think trumping up some Klingon atrocities, making it personal and immediate for someone, somewhere, would have been good.
Hell, maybe the Klingons killed Carol's mom when she was off doing something on a Federation colony. Instead of making it about vengeance though.
I propose taking a page out of The Doomsday Machine, and model Marcus off of the Decker mold. Decker was motivated by guilt and a sense of duty to protect the Federation, but his way of going about that was clouded and thusly desperate, foolhardy, and nearly got a grand total of 800+ people killed. I think some elements from that would have made Marcus a much more enjoyable and complicated character.
As it is I don't see anything "good" about Marcus. Well, okay, one thing. He did beam his daughter to safety. There's just no counter-balance to any of his bad actions. He's built a secret super death ship, plotted to start a war with the Klingons, plotted to kill an entire crew of innocent people, used Khan, and was fully prepared to secretly murder Khan's people.