The resistors are there to reduce noise. Resistors know nothing of direction of current flow. In a spark plug application, they are a part of a inductance, capacitance, resistance circuit and the high-speed noise is filtered by the additional of a little resistance. That resistance is minor when compared to the resistance of the plug gap and more importantly, non-existent to the current flowing through it to the plug gap.
Noise in the air can trigger various things in a digital circuit but is unlikely to physically damage it. Back current in the coil is high enough to destroy unprotected electronics but the resistance of the secondary has nothing to do with that and the designers of the EIs know to protects against it. Resistor caps/wires/plugs do increase the voltage needed for a spark to jump the gap, but there is plenty of excess voltage available so that's a non-issue.