It is actually possible to get redboot to boot an application without human intervention. The commands you would have typed at the console can be "scripted" in the redboot config data so that it will automatically download and boot an application. More detail on this can be found in the redboot manual (which comes with the eCos documentation).
However using Redboot in this case sounds like using a slegehammer to crack a nut. It sounds like you need to write yourself a simple monitor program which will sit in a loop waiting for a PIO to assert (or equivalent), and then jumps to the entry point for your application.
The PowerPC can then load the code and signal the Nios to start using the PIO.
I'd recommend that you write your monitor program as a HAL application using the alt_main() entry point.
This is more of a "push" rather than a "pull" model, which may or may not be apropriate depending on your system.