There is an additional factor. MLB contributes to the various collegiate summer wooden-bat leagues. They want to be able to scout the players in the wooden-bat situation, which they can't do in the regular collegiate season since the colleges and universities play with metal bats. Even if a court decision came in against them, they could cut off or reduce those funds. They'd be cutting their own throats if they did that, however; the Cape Cod League is widely regarded as the premier summer collegiate league as witnessed by the list I linked to above.