You do not have to build you're application to get a system.h file. It's tied to the system_lib itself. If you create the library for your NIOS build it and you're system.h will appear under here: hello_world_0_syslib\Debug\system_description (if you used the hello_world demo).
It's still requires a build but you do not need you're software to be even started to do that (when you develop software it requires at least 2 projects, one is the application itself, and the other is the system library project (so just build that))
G-luck