hi,
you're right in identifying that the iss is being over cautious by erroring on unitialized memory accesses. This has been identified as a problem and will be addressed in the next version. As a workaround for now though, edit the "clear_x_bits_ld_non_bypass" parameter and set it to 1 in the ptf file. This parameter should be located within the WIZARD_SCRIPT_ARGUMENTS for the nios2 module.
This will cause the errors to be output as warnings instead, so your program won't error out.
If you would like to suppress all the warnings altogether, when running the iss, go to the menu bar:
Run->Run... and select the launch configuration for your project (identified by the project name). Select the ISS Settings tab, and uncheck the Warning tick box.