So we all have either seen or heard of the controversial scene at the end of MOS. I have heard all these short term solutions, but we need long term, so here are my Ideas, and if you have anything better, you tree huggers better Spit it out.
Lobotomy: Superman could have used heat vision and gone this route but this is not very Superman like.
Amputation: Clark could have removed his limbs with his super strength after knocking Zod unconscious. But he is Superman not Leatherface.
Kryptonian Tech: What Kryptonian tech? Also I am pretty sure the dude actually raised on Krypton knows a little more about Kryptonian tech then the guy raised by farmers.
Freeze Breath: Really? Also did Clark know he could even do that? And again, Ice? Really?
Battlefield Removal: Clark could have knocked him unconscious, and tied him to an Astroid. But wouldn't being removed from our atmosphere turn Zod human, causing him to die in space? Even if not, wouldn't he starve to death? Again not a Superman like thing to do.
We'll those are my options, I dare you to think of something better.