No, Joe Quesada ruined the greatest marriage in Marvel Comics. Joe Quesada wanted to end the marriage and Marvel editorial told him that they were taking him off the book and revamping Spider-Man. They gave him the option of writing One More Day to be his last Spider-Man story and he accepted it. But he ended up being so dissatisfied that he ended up quitting and Joe Quesada took over the writing duties. Even though JMS' name was credited, Amazing Spider-Man #545, which ended the Spider-Man/Mary Jane marriage was 100% written by Joe Quesada. If you actually read the JMS' run on Amazing Spider-Man, he put a lot of heart and soul into their marriage and it's pretty obvious that he was against ending the marriage. Blame Joe Quesada on this one, not JMS.
Also, the issues of Superman that JMS wrote, Superman was rather polite to Lois. And the interlude issues written by G. Willow Wilson has Superman and Lois very much in love. The latest issue that was written by Chris Roberson, is the one where Superman is a total dick to Lois. So blame Chris Roberson on this one, not JMS. If JMS continued writing Superman, I think that Superman would have been a bit more respectful in his reasoning towards Lois. JMS' Superman was only a dick to those who really deserved it like the drug dealers in Philadelphia and the abusive father in Chicago.