Of course it was. Even in the face of articles being written about why superman doesn't kill no matter what and a producer known for not embracing the premise of comic books...
I'd be inclined to think it was an issue if it wasn't for the fact that this film was the first to shock the GA into a new take on the character. Perhaps I'll be more than open to the idea upon the sequel.
If only we could run an experiment where this was the first anyone had ever seen of the character, superheroes in general even. The film comes out and it get's the same scathing reviews....that would set the record straight that it's a matter of execution. For me anyways. Till then guess we'll just have to stick to our theories.
I don't care about Superman killing Zod. Zod put him in a position where had no choice. Not an issue as far as I'm concerned. All the destruction being glossed over at the end is annoying, but Avengers has its own issues at the end (namely all the villains dropping dead after Tony destroys the mothership, the same stupid copout that The Phantom Menace used).
What I do have an issue with is how everything between the destruction of Krypton and Zod showing up on Earth is a poorly-acted (except for Costner and Adams), convoluted mess. They try to copy the same style that was used in Batman Begins which show his early life, but unlike that film there is really no rhyme or reason for the scenes they chose (besides Jonathan's death and the way they handled that was incredibly stupid), and they are always awkwardly inserted into the modern day narrative. The Jor-El scene is reduced to meaningless exposition (most of which we already know from the opening Krypton sequences) and no real relationship is ever developed between Clark and Jor-El. Overall, it did a poor job on showing how Clark Kent became Superman. He was gifted powers from birth, has a five minute conversation with Jor-El, and he's Superman. There needs to be some sort of arc there and it was badly bungled. Everything happens too quickly and too easily, with a lack of emotion.
The last half of the film is much better, but the fight scenes still go on for too long. I was entertained, but I have seen far too many complaints about that by critics and just people I know to ignore that. People can only handle one CGI character punching another CGI character for so long before they get bored.
Probably the biggest problem I have with the film is Henry Cavill's performance. This film really needed someone charismatic enough to carry that role, and Cavill is just bland and wooden. One of my friends who is not a fan of the comics said that Cavill was perfect for the role because he is just as dull and uninteresting as Superman is in the comics. I happen to like Superman, but that's not the type of reaction you want to be getting from people. A lot of people actually seem to like Cavill's performance, which completely baffles me because I thought he was terrible.
So yes, I have far more problems with the film than it not fitting my pre-concieved notions of what it should have been. That said, I still enjoyed it. There was enough there in the opening 20 minutes and the last half that I liked it. But it is a deeply flawed film and I can easily see where someone who is not a fan of the character would not like it. Of my closest friends and family, I'm actually the one who likes this film the most.
It is an ambitious film that tries to recreate this character for the 21st Century (something that was badly needed), but unlike Christopher Nolan, Zack Snyder simply isn't skilled enough to reach those goals.