I think, if there's going to be Time Travel, it's going to involve Harry heading back to meet Papa Murphy and help him with a Black Cat case. There's a Word of Jim that basically confirms it wasn't a suicide; to me, that's an indication that we'll find out what really happened to him.
I could see a chain of events taking shape, with Murphy and Harry getting thrown back there by Uriel (or Mab, or whatever) because someone else was messing with time, like Nicodemus in a last-ditch attempt to pull off a win. They get stuck there for a while, baby happens, then get snapped back to the present, being forced to abandon their baby, who they find out is John Marcone. Because he's such an important figure, they can't go back and rescue him, or risk violating Time Laws by ending the loop (or I guess, in this case, opening a closed loop).
Super implausible, sure, but why not? If nothing else, there's a pretty good reason to end their relationship if Jim intends to do that.