The Game of Thrones season 8 scripts insinuated that Jon Snow was disturbed by his incestuous relationship with Daenerys Targaryen after he found out about their blood ties. Jon was finally filled in about his Targaryen heritage in the final season of the HBO series. Jon tried to act as though his identity as Aegon Targaryen didn't affect his feeling for his lover, but the original scripts suggested otherwise.
Jon first aligned with Daenerys in Game of Thrones season 7 when he asked for her assistance with the impending battle against the Night King and the Army of the Dead. After encountering the White Walkers beyond the Wall, and losing a dragon in the process, Daenerys agreed to help Jon. In turn, Jon pledged his allegiance to Daenerys as his Queen. It was clear that the pair had feelings for each other and they finally acted on those in the season 7 finale. By that point, Sam learned of Jon's true identity, which made Daenerys his aunt, but it would be a while until Jon himself learned the truth.
Daenerys and her forces arrived in Winterfell along with Jon in Game of Thrones season 8. Jon then learned that he was the son of Rhaegar Targaryen and relayed that information to Daenerys. Rather than being concerned about their incestuous relationship, Daenerys instantly realized that Jon was the true heir to the Iron Throne. After the Battle of Winterfell, Daenerys and Jon turned their sights to King's Landing. Daenerys became increasingly worried that the Westeros would prefer Jon over her but she never fully contemplated how Jon's heritage would affect his mindset. During "The Bells," Daenerys confronted Jon about his changed feelings. Jon claimed that he loved her but couldn't respond when Daenerys asked if he only thought of her as his queen. According to the Game of Thrones scripts available at the Writers Guild Foundation Shavelson-Webb Library in Los Angeles (via Insider), there was more clarity given in terms of Jon's disgust when it came to his romantic relationship with his aunt.
What Game Of Thrones Left Out Regarding Jon's Feelings Towards Daenerys
During the specific scene, Daenerys kissed Jon after he didn't respond to her question. He returned the kiss before he backed away due to their family ties. Daenerys realized what his reaction meant and proclaimed, "let it be fear" when recognizing his new feelings toward her. In the scripts, there was more context given to their encounter since the scene was expanded. When Daenerys asked if she was just a queen to him, nothing more, he responded by saying "no." They kissed but when Jon broke away, the script revealed that Daenerys was desperate and couldn't "remember a time she has felt this alone." She also recognized that Jon loved her but could no longer support her or the relationship. In the original script, Daenerys then stated that their romance now disgusted Jon, to which he couldn't find a reasonable interjection.
The original script further clarified Daenerys' feelings before her attack on King's Landing. There were obvious signs that Daenerys felt alone in her mission but this extended scene would have reiterated that notion by giving viewers more evidence into her mindset before ignoring Cersei's surrender. The final chapters of Game of Thrones would have also benefited by better revealing Jon's ambivalence towards Daenerys. He may have still been in love with his queen, but he no longer felt the freedom in continuing the romantic side of their relationship. That may have come into play when Jon felt the need to eliminate Daenerys as a way to protect Westeros.