I've decided that I am going to defend the Marlins and their ownership on this move.
Suppose you are the Marlins. You are one of the less profitable teams in baseball and your players usually leave once they are FA's, but you are pretty good at IDing and developing prospects, and you just spent a lot of money on FA's. But the chemistry or whatever just didn't work out, and you didn't contend with all those FA's on your team.
(1) Keep them and their backloaded contracts on the books, hoping that magic will somehow strike the same group differently, and risking those contracts becoming untradeable?
(2) Do something else?
The Marlins did something else. For whatever reason, the current crew wasn't getting it done, so they dumped them (along with players likely to become FA's and leave soon), reloaded with prospects, and cleaned up $80 million in payroll. Now, you have a new core to rebuild around, and the option to sign FA help around that core once you see a window opening up.
The Marlins, in my view, are one of the most shrewdly managed teams in baseball. It doesn't always work out, but they're highly Vulcan-like. Dismantling the 1997 and 2003 WS teams was shrewd: most teams don't repeat the same performance the next season and players are at their peak after a WS win. Compare the 1997 Marlins to, say, the 2002 Angels, who kept everyone and became a mediocre team.
They only have a repuation of developing good players, built on the back of Dave Dombrowski.
Look at some of the nobodys they've drafted in round 1 lately.