How to limit negative voltage on uC input pin
As Andy says the large negative pulse will break down the base-emitter (and damage the transistor), they are typically rated for ~5V reverse maximum.  

The idea you have isn't so bad, with a couple of component value changes it can work. Basically you need to increase the impedance going into the base, add a protection diode across the b-e junction, and lower the impedance at the output of the transistor (this makes it less susceptible to anything working against it, noise, etc) 

Also when simulating coils remember to include any coil resistance and parallel capacitance - this can make a big difference to your simulation (i.e. the reverse EMF will likely be much lower in real life if it's a big hand wound coil - if you have a LCR meter use it to get some measurements)

Something like this (I just took the relevant bits) is a start. Obviously the 1k and 47k resistors can be just one, I was following your schematic and was going to add the other bit but decided against it. The output to the uC is inverted but this it trivial to compensate for in firmware (or you can take the output from the emitter still if you prefer, with a lower resistor value):



Simulation:



One last thing - your uC input will tolerate a small negative voltage and will likely have some input protection (the details will be in the datasheet) so up to around -0.3V or so will probably be okay.