Names currently on the IL-60 or IL-FS that you didn't mention:
MLB: Mazur, Kempner
AAA: Tinoco, McKendry
AA: Meachem, Schomberg, Bragg, Vasquez
A+: Brink, Maldonado, Austin, Cardenas, Lashutka, Renner
A: Benitez, Rodriguez, Shepardson, Shunck
FCL: Defrank, both Polanco's, Wilson, Godoy, Jimenez, Montero
DSL: Guerrero, De La Rosa, Ortiz, Rodriguez, probably others
We only have 4 batters on the IL-FS. Pitchers are pushing their limits more every year. With advancements in technology, everyone now has the recipe to throw harder. It feels like every pitcher that throws 95+ is going to end up on the long term IL at least once every 3-4 years. It's not just TJS either. It's shoulders, core muscles, and leg/hip injuries due to longer strides.
If the Marlins could do something to prevent long-term injuries (without sacrificing performance gains), I'm sure they would do it. Minor league starters rarely throw 90 pitches anymore and only start every 6-7 days. Most MiLB teams have gone to a 6-man rotation. Only twice has a Marlins DSL guy pitched over 4 innings and none have completed 5. FCL is about the same. I count only 8 times a pitcher completed 6ip in low-A, and only once did they pitch in the 7th. Four of those QS were by the same guy (Genao).
Maybe the answer is to let them pitch more frequently, but less innings? Like throw 60 pitches every 4-5 days instead of 75 pitches every 6-7?