Oh, shock value was definitely a big part of it, but I think there were some deeper reasons to go along with that.
I think one of the big things is that Snyder wanted to challenge people's notions about who and what Superman is. There's tons of instances in the comics where Clark has taken a life (hell he's killed Zod in like, half a dozen different stories across various formats). So its not out of character, but the general public doesn't realize that. I think this was just one more way in which Snyder wanted to show people that Clark has more to him than what Donner showed us.
I think it was also about how far Clark was willing to go. How much would he sacrifice for humanity? How much *could* he? Clark had already destroyed the genesis chamber, ensuring that at least one Kryptonian tradition would never return. Clark had already killed Krypton's future for the sake of earth, would he/could he also kill its past? Sure, Zod was crazy and bent on genocide but he was also one of the only remaining Kryptonians in the universe. I don't think we can truly appreciate what it's like to be part of an extinct species, but it should go without saying that killing one of the only ones left must have hurt in a way we can't imagine.
The ramifications *should* have been explored. It *should* have had more of an impact in BvS. But if we're just talking about MoS, and not factoring in the other films, I think they handled it fine. The last couple scenes aren't places where Clark would be showing his pain; its not like he's gonna run up to the military general trying to spy on him and unload his emotional burden. Nor would he do that on his first day of work at his new job.
I mean, yeah obviously a huge part of the reasoning there was shock value, but I dont think it was the *only* reason.