It was getting very hot after sending 12v straight from the Vin to the gate of that transistor.
You were essentially powering the mcu at 11.3v. In experiments like that, you should have a small resistor there to just limit the current.
To make you feel better, avrs can survive 13v for a couple of seconds, at about 50% survival rate. at 12v, 80% of them can survive.
So there is a good chance that your arduino is actually ok. Those little fellows are not that fragile.