One idea could be that Clem somehow gets transported to the Naruto universe. Maybe she has to learn chakra control and ninjutsu to survive in this new world filled with shinobi. She could form an unlikely alliance with Naruto, given their shared experiences of growing up in tough situations.
One positive aspect is their mutual protection. Clem is always looking out for AJ, and AJ in turn tries to be brave and help Clem when he can. For example, in some fanfics, when they are surrounded by walkers, they work together to fend them off. AJ might use his small size to his advantage by getting into tight spaces, while Clem uses her combat skills.
Yes, there are many fanfics that focus on their relationship in a non - sexual way. For example, some might explore their survival adventures together, how they learn from each other and grow in the harsh post - apocalyptic world. These fanfics are more about their bond as friends or family, which is in line with the general theme of the show.
Michonne does die in the comics. The circumstances surrounding her death were quite dramatic and had a significant impact on the story's progression. It happened during a major conflict with other characters.