DDR2 interface between FPGA and MCU

I took a quick look at the MCU. (a deeper look requires a NDA ...) IMO the only DDR interface is the one to attach the main memory for the SoC. If you want to connect to this interface you will very likely have to use the SSTL-1.8 voltage drive, but furthermore the FPGA will have to act as a DDR memory device. Apart from your reasons to do so, the required interfacing will not be that difficult as the JEDEC DDR2 specification puts the difficulties at the controller side which in your set-up is the SoC.