The file that needs to be modified to activate auto negotiation is MCF52235_sysinit.c, and should reside somewhere in the CPU folder (left pane in CodeWarrior). The routine mcf5223x_ePHY_init is the one that enables the PHY and also does the link negotiation. You'll have to modify that routine by removing the software negotiation steps and set the PHY registers to enable auto negotiation.
Configuring the PHY is not a hard thing to do. The PHY registers are described in the 52235 reference manual. Remember to use the fec_mii_read and fec_mii_write functions to access the PHY registers.
I may also figure out the modification for you but that will take a little time, and I may not be able to test it out as my demo boards only contain the older device with the bug.