I think my first reaction to the end of #126 was similar to many of the views expressed here - I was disappointing that Negan wasn't killed. After re-reading the issue, and doing some analysis, I think I understand why.
First off - I'm pretty sure my disappointment comes not just from the fact that Negan didn't die, but I thought I had accurately predicted what would happen (Knife was poisoned, Negan's army falls apart around him, Dwight kills Negan w/ Lucille). We all know that Negan deserves death - and we all want to see Lucille get a taste of Negan.
However - I do understand why Kirkman kept Negan alive:
1. Keeping TWD unpredictable. Not that it's impossible to correctly predict what will happen... but I think most of us thought that either Negan or Rick would die and that would be the end of the war. It was hard to imagine the war ending WITHOUT a major death as in what happened in #126.
2. Negan is a great character. Very entertaining, and even if you think The Governor is a better villain - Negan still should get credit for being very fun and interesting. Keeping him alive gives us the opportunity to A) learn more about his backstory (which we all want to know about), and B- opens the door for great character interaction in the future. I want to see what Negan's WIVES have to say, now that they are free from his grasp. It would be great to see a conversation between Sherry and Negan (I think that will be in the works) now that the war is over.
3. It actually DOES play into Rick's plan of reconstruction.
Negan has been cut off from the Saviors, and they don't even know if he survived. As far as the Saviors are concerned, Negan's rulebook has been thrown out. Sure - Negan is still dangerous and may try to escape, but I believe that his real power lies in his leadership capacity. Since he has no one left to lead - his power has been nullified.
Also, even though Negan will be locked up - he can still be useful. Despite being a monumental prick - Negan is incredibly smart and has lots of survival information/tactical knowledge that Rick can use... if he can find a way to get to it.