How can I direct run nios programmer on epcs?

Years ago back in the nios forum days someone posted an EPCS controller that would allow you to do this. Mind you it would be incredibly slow and you don't want to use it for rwdata, heap, or stack otherwise you'll kill the Flash cells pretty quickly.

If your board is still in development I would recommend slapping a x8 DDR SDRAM on it since even if you get a controller that will allow you to run code in place out of flash, or page in code it's going to be pretty slow.