I don't see how Bryant's case has much to do with production, and it has zero to do with free agent contracts (like Kimbrel's), except for the fact that he's being denied the chance to enjoy the open market himself for one more year. The big money and guaranteed contracts good players do get to enjoy as they hit their prime (and eventually, albeit, still slowly, free agency) are already supposed to be the carrot at the end of a very long minor league stick. Lengthening the stick is just further unfairness.
For the first few years of his career Bryant (and everyone else) gets paid the same whether he's good or not, and while arbitration provides a certain amount of baseline security, if a player isn't good they will either miss out on the big raises or be non-tendered (or won't stick in the majors in the first place).
Make players free agents after two years and I'm sure they'd also be happy to have some non-guaranteed components to the contracts - they already play on what are essentially non-guaranteed contracts for 6-7 years (at least from season-to-seasons), so why not?
The rules are the rules, yes, and when a player deserves to be called up is always going to be open to interpretation (and in extreme cases this is also why they have Rule 5). But the manipulation here was obvious. I don't think you can say the same about Franco and couldn't about Bohm either. Even Kingery could have plausibly been sent down two years ago (especially in hindsight).
The Cubs also missed hosting a wild card game by 1 win, and hosting the NLDS and NLCS by three wins, though as it happens they still won the first two rounds (and lost to the Mets so decisively it probably didn't matter). Bryant probably wouldn't have added three wins in two weeks either.
This actually strikes me as one of the easier and less controversial things for the CBA to fix. The union should probably have its eye on bigger goals (such as actual earlier arbitration and free agency) rather than just massaging the timelines.