You’ll have to do it yourself and write a custom bootloader for the Nios CPU that would decrypt the stored software on the fly. But why do you want to do that and what do you want to protect the software against?
You will need in any case the decryption keys in the bootloader itself so anyone with enough skill and motivation should be able to find the key and decrypt the software anyway.
The ones that start with alt_ seem to be the problem. Is this a result of having no program data to go into the section?
I can use a define from system.h for my immeadiate problem but this has got my curiosity up and I'm likely to need access to some of these linker generated symbols in the future. Any help appreciated.