Well, I see it like this:
1. IF Freddie continues to play as well as he has the last few years, then he will be in demand for a 4-5 year deal in the $100-$125 range, about what JD would have gotten if he had not been hurt leading into last year. By that time, I expect the DH to be in play for the NL, so that box will be available for a Freddie slowing in the field. But, as you say, 1B isn't the smartest area to put a lot of money commitment in the long run so his demand outside Atlanta will probably be forced down a bit as a result, especially if the QO is still a thing and the Braves place it on Freddie. So, in this case, I would see him back in Atlanta for about a 4/$90 with a year 5 option at $20M.
2. If Freddie gets hurt or doesn't play as well, then he likely goes Y2Y with the Braves or accepts a QO in hopes of going the JD route.
3. If the BRaves do sign JD, I would expect the likelihood of re-signing Freddie actually diminishes because AA would have to be thinking about the DH/1B for the last 2 years of JD.
4. This situation is what I was forecasting when I was pushing to trade Freddie, given the right return. He currently commands $22M of the payroll and is rolling into his last two years of control. He's worth the money but he eats payroll space, limits flexibility somewhat and presents future payroll dilema. If the Braves had traded him after 2016, as I suggested, for (assuming Astro agreement which at the time probably wasn't out of the question - remember Houston was into their window and showing huge promise) Tucker, Whitley and Alvarez, which I did (Tucker was #8 prospect according to MLB 2017 list, Whitley was #36 and Alvarez was unlisted), then Alvarez would likely be standing at 1B at the ML minimum and Tucker would be starting in RF at ML minimum and Whitley would be in AAA with huge promise, the best pitching prospect in the Braves system.
Of course, without Freeman, the Braves wouldn't likely have won the East either of the last two years and might not have been able to sign Acuna or Albies on the contracts that they are on. We will never know.