It is a mistake in the manual that has been already fixed. Please take a look at the manual errata (MPC8349EARMAD), it states:
"9.4.1.8, 9-23 Changed setting 01 of DDR_SDRAM_CONFIG_2[DQS_CFG] to reserved."
So no, differential DQS is not available and can not be configured in the MPC8349.
It is a mistake in the manual that has been already fixed. Please take a look at the manual errata (MPC8349EARMAD), it states:
"9.4.1.8, 9-23 Changed setting 01 of DDR_SDRAM_CONFIG_2[DQS_CFG] to reserved."
So no, differential DQS is not available and can not be configured in the MPC8349.