How about this:
Lee is not dead. His yellow eyes are a sign of infection, but not zombie infection. Instead they are a sign of a general infection from cutting off his arm. For those who chose the option of Clem shooting Lee. She doesn't do it. Instead she shoots the handcuff chain--in the comics Morgan did this when leaving his son Duane who had become a zombie behind. He had him restrained and had become very unstable when Rick and company found him. He was supposed to put his son out of his misery and then join them. There's a gunshot, he joins them, and they leave but then you see his zombie son leave the house--in other words he shot the restraint.
Clem shoots the handcuffs because she just can't shoot Lee and leaves. He is in a secure area. He passes out perhaps even enters into a coma like state allowing his body to fight the infection.
My theory is far fetched I know, and I'm not sure how he would get out of the cuffs for those who chose Clem not shooting him.
Anyway, just had that random thought and wanted to add to all the wonderful dialogue going on.
Great game and looking forward to Season 2!