The biggest problem with the CE FA is the clueless (who don't learn no matter how many times the clues are handed to them) and the griefers (who fly in to die just to annoy everyone else). The real problem here is not that these players are present in the Fleet Action ... the problem is that they cannot be ejected from it.
When your ship is destroyed during the Crystaline Entity Fleet Action, the Respawn Timer tells you ... in advance ... that your ship will be respawned at Starbase 39. And when you respawn, you are indeed in orbit around Starbase 39 just as if you had Beamed Up To Ship from inside the station.
Net Effect: Culling the stupid/obnoxious.
Anyone who "allows" their ship to be destroyed (and thus almost certainly "feeding" the Crystaline Entity) gets ejected from the Fleet Action to destroy the Entity. They can always return to the Fleet Action ... by warping out from Starbase 39 to Sector Space, navigating Sector Space back to the Deep Space Encounter with the Entity, entering the Fleet Action and returning to the battle ... but it'll take a lot more EFFORT on the part of people who "sacrificed themselves and their crew" to FEED the Entity. Enough "effort" (I would hope) to encourage them to LEARN how to fight the Entity and not just suicide into it repeatedly (because there is no Death Penalty).
Anyone who "stays alive and fighting" of course gets to stay in the Fleet Action until the Entity is defeated.