High Current return path
It is really hard to say what killed your CPU.  But here are some things that are either certainly wrong or something to look into.


I assume that you are using an N-Channel MOSFET.  Your schematics are not clear about that.
You do not show how you are powering the opamp.  If I were doing this, I would power the opamp from +5v and -5v.  Alternatively, you need to make sure that the opamp inputs and outputs are not too close to the power rails.  The way it is currently drawn it is possible that the opamp will not be able to turn the MOSFET completely on and/or completely off.  
If you simulated this circuit using real models for the MOSFET and Opamp then you might find that it is unstable.  (Or check this with an o-scope.)  A cap between the opamp output and the negative input of the opamp could improve things.  It will take a little trial and error to find the correct cap value, but expect it to be in the range of 50 to 500 pF.  When I say "unstable", I mean that the output of the opamp or the LED current will oscillate or ring when it shouldn't.
Consider the parasitic capacitance between the pins on the MOSFET.  In particular between the drain and gate.  As the MOSFET turns on that cap will tend to force the gate voltage down.  If the Opamp were not there the gate would go to -20v.  With the opamp it won't be so bad.  It might not even be an issue.  But if the MOSFET is very large then the parasitic capacitance will be large and might overwhelm the opamps ability to drive the gate.  You don't need a large MOSFET for this circuit.
Consider the loop area of your circuit.  Your current loop is from the cap, through the LED/MOSFET/Resistor and back to the diode.  The square inches (cm) of this loop of wire has a direct influence on the amount of EMI that will be emitted.  Reduce the loop area to reduce the amount of EMI.  It might be possible to emit enough EMI to damage other circuits.
Consider placing a small cap in parallel with R2.  This will slow down the LED turn on/off time and thus reduce some of the bad effects of having that 5 amp current spike.  Of course don't slow it down enough to make your circuit not useful, but slowing it down even a little can help things a lot.
Place a current limiting resistor in series with your LED.  Size this resistor so that if the MOSFET is fully on the the LED is at around 110% of max power.  This will help make the circuit more stable and help keep you from accidentally blowing up your LED's.  It might be possible to combine this resistor with the current sense resistor (same resistor does both functions), but it depends on the input voltage range of your opamp.
Keep the high current path (Cap-LED-MOSFET-Resistor-Cap) wires short and thick.  Especially short.  These wires will act like an inductor, and the inductive kickback of 5 amps for 100 uS could be huge.  Also, you should put a high-current schottkey diode between the source and drain of the MOSFET.  There is already a diode in the MOSFET but it isn't that good.  Putting one in parallel with that will improve the protection from inductive kickback by a lot.
Carefully analyze the current paths of your circuit and change it to keep the high current and voltage spikes from the sensitive parts.  It is very likely that all of my other points will not identify what is causing the damage.  But it is just as likely that whatever is damaging things is happening on every pulse, but only does damage occasionally.  Get out the o-scope and methodically go through things.