What do you mean by robust spike suppression, and what do you mean by protecting the input?
Since the spark plug signal is tens of thousands of volts, and the input of the Arduino will be damaged or destroyed if the input voltage is less than -0.5V or greater than Vcc+0.5V, you have a problem to solve.
It is extremely likely that electrical noise from the engine is getting into the Arduino circuitry somehow. The schematic diagram posted is incomplete and does not have any protection for spikes getting into the 5V power supply, or even the ground connection.
Please post the rest of the circuit diagram, showing how the Arduino is powered, connected to the input circuitry, and how it is grounded and isolated from engine electrical noise. Everything but the electrically shielded sensor wire should be in a grounded, conductive enclosure.
The posted scope image tells me nothing, but I wonder what the nasty spikes on the blue trace mean.