HCT is open to interpretation. I admitted as much, then went on to explain my interpretation. But the affair didn't end in a relationship between Scott and Emma. HCT did that. Before HCT, no Scott and Emma relationship. After HCT, Scott and Emma relationship. It's entirely binary. HCT clearly shows us a Scott that was exiting all things X-Men, including Emma. Logan explains it all to Jean here:
By the end of the issue Jean had pulled her PF strings and the exact same panels are rerun with Scott choicing to stay with the School and with Emma. Exactly what Jean did is arguable. The end result is not.
The affair on is own did not lead to Scott and Emma's relationship. It lead to a disastrous future. Jean's interference lead to the relationship. This isn't really debatable.
As for Scott having always been self-loathing and insecure, I find you're argument on that point mind-boggling. Scott has been consistently portrayed as lacking in self worth since the Silver Age.
Scott doesn't believe he's worthy of leadership but Charles does and forces the point (UXM 7)
Scott doesn't believe can compete with Warren for Jean's affections, nor does he believe he even has a right to do so. (UXM 14)
Scott's self loathing again surfaces in the first several issues of X-Factor culminating in him ending up a drunk living on the docks of Long Island. Screenshot limits prevent me posting that, but I think you'll recall what I'm referring to.
Post "The Twelve" Scott refuses to be honest with Jean about his thoughts because he fears they will drive her away, leading to him confiding in Emma. People focus on the confiding in Emma part, but it's his failure to believe that Jean will accept him that is the underlying driver. Emma points this out to Scott herself, telling him that with her there's no judgementa and nothing is taboo with her. Emma understands that what's driving Scott and Jean apart is Scott's insecurities and she leans into that heavily to drive the affair.
After Jean's death in Planet X, Scott's so wracked with guilt and grief that he folds up on the X-Men permanently.
In Whedon's Astonishing X-Men #1, Logan confronts Scott over moving on so quickly with Emma. This leads to a fight on the front lawn. Scott loses control here because part of him continues to feel guilty about what he's doing. Not the actions of a self-assured individual.
As time goes on, Scott's pre-existing insecurities are compounded by the choices he's made that he regrets. This becomes a deepening cycle of regret and remorse, culminating in Last Will and Testament, where Scott doesn't feel he deserves to be Charles' heir.
Scott's only confidence comes through his leadership abilities. When the mask comes off, the insecurities always override his sense of self-worth. This is one of Scott's most defining features.
No, you don't have to share that view. I've already made my case for why Scott is, on balance, a hero. Scott's relative "worthiness" when it comes to Jean comes entirely down to how the writers perceive that Jean percieve's Scott's actions. Given her ability to overcome her concerns about Scott's behavior during and after the DPS and his marriage to Maddie, I perceive that Jean understands Scott's motivations and accepts his flaws. That's also been true since the Silver Age. I think she knew exactly what she was getting into with Scott, especially over time, and on balance decided that the positive outweighed the negative. After all this is a woman who as at various points believed herself to be the greatest mass murderer in human history. She understands guilt and how it can effect self-worth. Even though she didn't succumb to that guilt, I suspect she knows that Scott doesn't have to the tools to deal with that, given his in-built insecurities.