Nios - II memory alignment issue while accessing integer from non word align location

I'm afraid you will have to go through the LUFA code and change all the places where unaligned pointers are used. To help you, you can use the -Wcast-align option in gcc and it will generate a warning each time it thinks an unaligned transfer can happen.

IIRC unaligned transfers trigger a bus error on some ARM architectures also so it's really not good practise when making portable code.

GCC for ARM has a -mno-unaligned-access option that will automatically convert unaligned accesses into multiple byte accesses, but unfortunately it doesn't seem that this option is available for the Nios II architecture.