Has anyone pursued this further?
The standalone Quartus programmer works great for pof,sof,jic, but I need the ability to download an srec or binary file (u-boot) to sram and have it execute. As far as I can tell, the Quartus programmer can't do that. Right now I use nios2-download from the Nios tools, but the 400MB+ install for this one feature is undesirable.
I see two ways. The first is to take the nios2-download script and figure out the minimal set of components needed to support it - maybe cygwin plus the jtag drivers.
The second is to figure out how the jtag interface to the nios works and write some code to send the data directly.
If anyone has any success with either of these two methods, or some other obvious method I have missed, please post.