The way JMS played about with that aspect was one of the highlights of his whole run. He made Peter and MJ work harder than ever to come to an even greater understanding of their relationship and had to face some pretty painful issues in regards to mild paranoia and self-confidence, they experianced new hurdles and realized just how much they cared for one another as they leapt over them. The resolution to the seperation is just about the peak of his entire run (I still think he should have left with Romita Jr following Book of Ezekiel). It's a shame the last seven years have eroded all the hard work Peter and MJ put into sustaining that relationship, but then, it's easy to blame all of that negative stuff on chaos magic and Mephisto's influence (at least in my headcanon anyway)
You might want to read the last few days worth of the daily strip. Spidey and Jameson have buried the hatchetNo matter how much good he does JJJ will always hate Spider-man.