I have no problem with innocents dying, it's just about the set up.
I want Superman's world to have some realism, and I have always found the most interesting struggle for Superman as a character (that people say is too perfect) is that he CAN'T save everyone.
But what makes that work, and what makes it more poignant, is when you actually see that struggle.
When you see him save SOME people, while not being able to save everyone.
For example, you could show him swooping in after a train has de railed or a building has blown up or an earthquake has hit a town, and show him rescueing survivors trapped in aftermath.
There could be a visible body count, and you could even show how his eyes linger on them because of how he feels about not having been able to save them, but he is still able to save all the people still alive in there who might have died otherwise.
I think the problem people had with the assumed body count in MOS isn't that there WAS innocent lives lost (because it'd be illogical to think this movie based in the real world could turn out any other way really)... It's just that it wasn't acknowledged.
And just like I feel his conflicted feelings about having to kill Zod could have done with a small amount of dialogue, I think the 'all those people died, and I couldn't save them' would have been a good addition to that.
And both of those things seem like they would have fitted PERFECTLY in the Martha and Clark scene.
Missed opportunity to drive home some of the messages the film was trying to make if you ask me.
Which was 1. Sometimes even Superman has to make the hardest choices and 2. Even Superman can't save everyone, but that doesn't mean the people he does save mean nothing!
Both of which, in a well written script, could have come directly out of Martha's mouth (which I would have loved because it would help show the encouraging influence the Kents have on him being a hero).