Yes, Peter probably thinks about Jean/Ned less because he has no reason to feel guilty about their deaths. Jean was killed in her bed by a madman with a gun, and Peter had never encountered that murderer before Jean's death. Ned was set up by the Hobgoblin to be killed by the Foreigner while on a business trip. I guess there's a stretch-argument to be made that if Peter had captured Hobgoblin or Foreigner on one of their earlier encounters, he could have prevented Ned's death - but the guy shouldn't lose sleep over a logical stretch like that.
Then contrast the deaths of Ben Parker and Gwen Stacey. Ben was killed by the guy that Peter selfishly refused to stop when Peter encountered him moments earlier. Gwen was arguably killed by Peter himself when his webbing snapped her neck (the Goblin was ultimately responsible, but Peter doesn't think that way).
So in terms of long-term effects on Peter's psyche, the deaths of Ben/Gwen are far more impacting because of Peter's direct involvement, as well as the fact that he was much, much closer to them (a parental figure and the love of his life).
I also think any "moratorium" on Clone Saga references, if it ever existed as official policy or just something writer chose to avoid, has long since past. Since Brand New Day, there's been no shortage of Clone Saga influenced stories. Everything from the re-introduction of Kaine to the literal re-telling of the Clone Saga and a bunch of stuff in between. The current Spider-Verse issue even has an alternate Ben Reilly in it.