He has a pattern of deciding that she can't understand his Ginormous Box of Pain and cutting her out to rescue/whine to/screw someone else.
I'm still laughing at the SoapNet reruns from 4-5 years ago where Natalie mourns John like crazy, realizes that he is alive and it's Hugh who is dead, and plays nursemaid to him... only for him to announce that only Fake Marty understands his pain and that furthermore Fake Marty "has it together" (ha!) unlike Natalie.
I really hope that the rumor about Natalie/Liam getting killed or "killed" to further expand John's Ginormous Box of Pain isn't true. Viki, Clint, Roxy, Kevin, Joey, Jessica, Bree, etc., shouldn't have to lose Natalie over John's new romance. She's more than John's appendage.
And if John has become a Worshipper of Sonny and Mob Apologist, I really don't want Natalie or Liam around him anyway.