Thank you for this beautiful defense of Jean. I haven't read the Krakoa era so I don't have the same closure you do. I still cannot forgive Scott for his sins against Jean and frankly, I think some things are unforgivable. It's not just one thing but multiple as you've eloquently listed out. With comic book continuity, where time never passes and writers often ignore what other writers put down on the page before them, it's easy to move along and ignore prior history. But if Jean and Scott were real people and he did all these things to her, I'd warn her to go as far away from him as possible. He's bad news, all the way back to when he couldn't mourn her alleged death and was already looking at Colleen Wing. It took Storm to call him out and she truly showed more affection for Jean than Scott ever did. Similarly, how quickly he moved on after Jean's real death with Lee Forrester was also disturbing, enough that fans were shocked and horrified and poured into the letter pages to display their contempt for this. It's also implied that Scott and Lee were intimate on the island when they were stranded and alone together. I found that odd too since Scott is relatively shy and it's implied that he and Jean only consummated their love during TDPS (UXM #132). Classic X-Men backstories seemed to suggest that Jean's date with Scott on Christmas (UXM #98) was the night they were first going to consummate their relationship. So the fact that they only were intimate once after years of a relationship, but right after her death, Scott's already shacking up with Lee rubbed me the wrong way and others as well.
Perhaps the Krakoan era redeems him. I'm not sure. I now see Logan as not only being a better fit for her overall personality but also one who has never wronged her like Scott has repeatedly. Lorna fans have realized how toxic Alex was to Lorna since she's always wronged by him no matter the era or writer. I'm seeing the same with Jean and Scott and both women should be kept safe from problematic Summers brothers. Someone should go back in time and tell Stan or Roy Thomas that Jean should be paired with Warren because she'll be spared so much harm in the long run. Not to mention, being fridged for 14 years, which Joe Q literally said was done to develop Cyclops so he could hook up with that fake blonde hussy. MJ got the same treatment with OMD so it's not even exclusive to Jean.
Also being linked to Wolverine has helped Jean in the long run. Had Joe Q not refused to let Jean come back, she could have been on the New Avengers with Wolverine, Spider-Man, Captain America, Iron Man, Spider-Woman, etc. In the movies she got more screentime because she was Wolverine's love interest and the trilogy's epic love story. She was able to appear in more films than just the trilogy because of her role in The Wolverine. Now the Insomniac video game will give Jean a new huge platform and co-star status as the second most important X-Man after Wolverine. The Spider-Man Insomniac games have outsold all the Batman Arkhan games, despite the Spider-Man games being exclusive to Playstation so imagine how the Wolverine game will sell. Wolverine will always trump any other love interest because he's the second most popular Marvel character of all time after Spider-Man. In the Wolverine thread, it's even mentioned that his solo book outsells Batman and is second to only Spider-Man's solo, which is why Jean will always benefit from having her name linked to his, which is already the case in popular culture where people see Jean as Wolverine's girlfriend or ill-fated love. Even as far back as the late 90s, Marvel confirmed that having covers where Jean and Wolverine kiss always boosted sales so it shows what's really popular with the masses.
Renew Your Vows was a wonderful way to see both of Marvel's two most popular characters in happy marriages and equal partnerships. Would like to see more Jean/Logan children besides just adorable Kate. Jean is already in the running for being Marvel's most popular female character (I'd say Storm and Wanda are the other two most likely contenders) and having her name next to the second most popular Marvel character of all time (and presumably third or fourth most popular comic book hero) just cements that.