Marlin got this big fancy house for them, but it's clear that even it wasn't going to be large enough for all those kids when the eggs hatched. Marlin would have had to get a whole lot more territory -- in an area, as Clair and Marlin noted, that's in high demand. Did Marlin realize what he was getting into? Did he panic when he understood the depth of his current commitments?
I wonder what tracing Marlin's associations back would show. Did he have an insurance policy on Clair? Was the appearance of the barracuda an accident, or a clever setup? Did he have some fishy connections off-reef to organized crime schools, who might know where you could find a hit-fish?