Common ground circuit on Raspberry Pi blew fuse?
The transistor E-B junction is forward biased from the +9V input, which puts 9V minus a diode drop on the Raspberry Pi input, which will indeed damage it. So it did exactly what we could have predicted it would do. If a fuse blew, your abuse of the GPIO probably caused the entire chip to latch up, drawing very high current and causing a silicon firestorm on a chip-wide scale as many thousands of transistors lost their lives in a matter of milliseconds. 

It might have been possible to get this to work with a PNP transistor (by tying to the 3.3V supply since your motor supply is isolated) but I would strongly suggest using a logic-level n-channel MOSFET with some gate resistance in series, like 10K. The usual circuit looks like this. 







simulate this circuit &ndash; Schematic created using CircuitLab

R2 is to emphasize that the high motor current flows through the wire from the battery (-) terminal to the source of M1 and not through the RPi. The Schottky diode D1 is to absorb the inductive kick when the transistor turns off. 

Note: The MOSFET part number I show is an SOT-23 type. There are few through-hole MOSFETs guaranteed to work well with 3.3V drive- you can use a breakout board if you find the part a bit small to work with directly.