Well, Negan's end in the comics isn't straightforwardly due to one specific killing act. It's more complicated and involves multiple factors and characters' actions.
Well, it's hard to name the 'best' as it depends on personal taste. But some authors who are quite popular in the Carl and Negan fanfic community are those who really capture the complex relationship between the two characters. One such author might be someone who goes by the pen name 'WalkingDeadFan123'. Their stories often explore the psychological aspects of Carl and Negan's interactions in great detail.
Negan might protect Carl out of a sense of respect. Carl has shown himself to be a strong and determined character, and Negan could admire those qualities.