Hi Mike,
I suppose it depends on your system. If you are using EPCS serial flash, it may be possible to get away with using only the (free) Quartus standalone programmer. I think this is just a free Altera download.. if any license is required there should be no cost (send in a nic or hard drive ID and get a license file by email, if anything).
The procedure is to (on a computer with all of the dev tools installed) roll up the fpga .sof file and software .srec file into a single file that the programmer can use in a production line situation... I recently helped out a customer (added some conversion functionality into nios-convert) that went into 1.1 for this purpose, which converted our .srec into i-hex that the quartus convert programming files utility uses to combine data into a single programming file. Since it requires several steps to perform it is not a highlighted feature though.
If you are using parallel flash and aren't programming flash in some conventional programmer before soldering onto the board, then your idea bout using the command-line nios2-flash-programmer tool is a good one. This will still require installation of quartus + nios to get all the tools in place, but you can feel free to experiment with the flash programmer java executables if you'd like in order to run in a more standalone mode (quite honestly I don't know if this will work -- but it sounds like its worth a try)... even if that does not work, I don't see any reason why you should need a license file for it to operate as command line tools such as the flash programmer aren't doing things like HW compilation or generation, which do use the license files
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