Yes, D9 is for the LED. And D8 is for the FLASH if you have it. I would use another pin. Please see the pinout diagrams at moteino.com
I'm using an Arduino Uno with an ethernet shield on it, which is the reason I need to change the default Slave Select pin for the RFM69HW on the SPI bus. So I'm not using the Moteino sketch.
But the way I'm going about it, simply replacing SS on the header file with "9", doesn't seem to be working, and I'm doing this as a test without the ethernet shield on the Uno - it's just the Arduino and the RFM69HW, with the NSS pin on 9.
I see other people on this forum have done it before, but it's not clear what they changed.