Yes the Reconfiguration Controller's MIF Streamer supports byte and word addressing modes in Stratix V GX devices.
Byte addressing is the default mode. To change the addressing mode in the MIF Streamer, modify bit  of Streamer Module Internal MIF Register Offset 0x1 as detailed below.
Table 1. Streamer Module Internal MIF Register Offsets
Offset Bits R/W Register Name Description
0x1  RW MIF addressing mode Specifies the MIF addressing mode
1 = word addressing
0 = byte addressing
The Quartus 12.0 and earlier versions of the Transceiver PHY IP User Guide does not document how to change addressing modes and will be updated in a future release. For more information on the reconfiguration controller refer to the Transceiver PHY IP User Guide .