I am not a big fan of Superman's not trying to save people in MoS, and not trying to find a solution other than killing Zod--but accepting that that happened and given his remorse over doing it, I can see the following as part of the plot of the upcoming movie based on what I have seen so far, including the obvious Dark Knight Returns references:
Batman is grieving over failing to save Dick Grayson and other mistakes. He is taking the moral high ground and going after Superman who he sees as a grave threat to humanity. In the process, he basically doesn't care about killing criminals or other threats as long as the goal is achieved. He is probably beating himself up for not killing the Joker and has renounced his "no killing" policy.
In his earnestness to take down Superman, he fails to see that he--Batman--has become the very thing he is fighting against.
Eventually he learns that Superman is not the bad guy and feels genuine remorse over his failure in MoS. In return, Superman teaches Batman that there is a better way to be a symbol of good and of justice in the world, hence Dawn of Justice.
I would be surprised if the movie does not develop along these lines with this sense of redemption at the end and Superman being the virtuous Superman that defines the character.