I regularly use 9V batteries for field testing of Moteinos, and just like you mentioned, I simply apply the 9V to VIN, and everything works great, every time.
Again - 9V, 12V and even more, applied to VIN, will never damage a Moteino. The MCP1703 regulator has a max limit of 16V. This is true for ALL Moteinos except the Moteino-8Mhz which has no regulator.
I did reset the device but nothing changed.
When you reset the device, it enters the bootloader and flashes the LED a few times. Did that happen?
Otherwise I cannot tell what really happened without having the unit in front of me to tell what parts are damaged. You are welcome to send it to me and I can take a brief look at it, if that is worth it for you.