I think both things will happen - and I've long stated, the DCEU will make more sense as more movies get released.
I don't feel they wanted to delve that deep into superman just yet, he's a rookie, and as such will be treated this way - he's testing his powers in MoS, his moral views are what he's learned in smallville, him killing Zod is due to his lack of experience.
In B vs S, his moral views are starting to be tested, he believes he's doing good, but now the question comes up what is good.
By MoS 2 (or maybe in JL)
I imagine we will see a much more refined superman, who can differentiate these moments, and understand how to do the right thing.
The pay off will be huge if it's executed correctly, but the problem I'm finding is (as in todays society) is that everyone wants everything "now."
I guess, I first noticed that with the first 3 spiderman (with Tobey), every movie felt like it was more him dealing with the same problem on how to deal with being peter parker and spider-man. (I liked the movies.) but it kind of got old, especially when I see the "amazing" spider-man, where it felt like it was going down a very similar path with the character.
I shouldn't need to see that story so often, and I feel in that sense DCEU is going for a different approach to their characters, the only one I truly question at the moment is Batman, because I feel a Batman that's already gone through a robin(or 2), well, would approach things differently than affleck's batman did.