One challenge is the complex and often dark nature of their relationship. Thanos is a villain who has done terrible things, including to Gamora herself. So, it's difficult to make their relationship believable in a positive or even a nuanced way.
It's not okay at all. Fanfiction should be based on positive and ethical interpretations. Thanos is a villain, and Gamora has her own story arc that doesn't involve this kind of inappropriate relationship. Moreover, this kind of content can be disturbing to a lot of people who love the original franchise. It's better to focus on creating fan works that explore the characters' growth, their battles, and their relationships in a proper and respectful way.
Another storyline could be an alternate universe where Thanos has a change of heart due to Gamora's influence. Maybe she shows him a different way to 'balance' the universe that doesn't involve mass destruction. This could lead to a series of events where they work together to reform the way the universe is governed.
There are several negative impacts. Firstly, it is morally wrong as it involves improper and unethical content especially considering Gamora's character. Secondly, it can have a negative influence on the perception of the characters in the Marvel universe. People may start to view Thanos or Gamora in a wrong and inappropriate light. Thirdly, it can lead to a division in the fan community, with some fans being disgusted by such content and others maybe wrongly thinking it's okay.