You can access the PIO regs file by just adding the following include paths to your compiler flags:
-I'$(SOPC_KIT_NIOS2)'/components/altera_avalon_pio/inc -I$(PREFIX)/include/cyg/hal
As far as how to connect to an interrupt, you seem to have answered your own question in the code you posted. You connect by making calls to the three functions: cyg_drv_interrupt_create(), cyg_drv_interrupt_attach(), and cyg_drv_interrupt_unmask(). Details on how to use these functions can be found in the eCos documentation.
Whether you do this in a similar manner to the count_pio example, or write a full blown driver is up to you (although I might be inclined to go for the former). If you do want to create a DEVTAB entry, then take a look at: packages/devs/touch/arm/ipaq/current/src/ipaq_ts.c for a simple example (that's the IPAQ touch screen driver).
Finally, in the spirit of open source development, if you do come up with anything that you’d like to make available to others, or maybe even see in the next release – please post it to this forum
http://forum.niosforum.com/work2/style_emoticons/<#EMO_DIR#>/smile.gif