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

This is not due to Eclipse, it is a limitation of the Nios II architecture that does not support unaligned accesses.

But anyway, please note that using an unaligned pointer accesses is "undefined behaviour" in the C standard, so your code could return anything and still be 100% correct according to the C standard. This kind of construct is not portable because it can work on some architectures and not on others. It could even work on some compilers and not others.