The problem is it's NOT a shared cost from QF's point of view.
Basically as far as QF is concerned with the ticket you got from NRT-SFO you'd be a no show for that sector due to .. well reality is they don't care the reasons why. With no availability (and limited rerouting, if any, options) then they could, and did.. (panfully) walk away from it. Seems like JL proposed very reasonable solution, but their hands are tied because you only purchased a ticket with them from MEL-NRT - which they were operating, but horribly delayed (I think had they cancelled that flight, the situation might be slightly different, but still problematic imo). See, you could have still taken that flight to NRT you purchased.... (and well being stuck in MEL with no flights is probably better than being stuck in Tokyo I would think).
As others have said this is the incredble risk with separate tickets - even if on the same airline. JL is correct in that they couldn't touch the QF issued ticket, even though it's on their flight and QF clearly wouldn't come to the party - I understand why of course but it's a coughpy outcome even if the "rules" have been met per se.
In theory this is where a far more unified oneworld coordination system would help - or perhaps from a customer perspective SHOULD help. I mean they're an alliance in theory but the two parts aren't behaving as part of the alliance that's supposed to look after their alliance customer. Disappointing.
As per other comments this is where padding, and a lot of it, and/or flexibility is essential.
it occurs to me that if JL were saying the NRT-SFO flight was oversold - would they have been willing to move you to the next day or something like that I wonder - helps them out and you'd make that connection. QF would probably not have a problem with that. Now you may not have been able to make an overnight in NRT and a delayed arrival in SFO work for your plans (christmas) but seems to me that might have been an angle to potentially work on. Of course it's easy for me sitting here not stressed out and annoyed that my trip has been nuked.