Apart from what vanhelzing said, I think there are too many effects going in one direction and only one going in the other.
Currently(and even with the HP system around) there'll be 2 damage "sponges", hull and shields (both HP in the HP system and the blocks themselves are counted as hull). Pierce, punch-through, explosive, missiles as primary, pulse as primary, cannons as secondary are all designed against hull. Some reduce shield damage, buff hull damage or reduce the wasted damage dealt to an already dead block. The only effect that is designed against shields is ion. How shall the ion effect "balance" out pierce, punch-through, explosive, missiles, pulse and cannons? And since some primary weapon systems are balanced against hull, all effects and secondaries applied to them are too. The cannon as a secondary is also balanced against blocks as it increases RoF and thus reduces the damage wasted on a dead block, turning all primaries and effects applied to them against hull too.
A viable way to prevent this? idk.
In case of pulse as a secondary I can thing of something:
the damage-increase curve has a sharp upward bent right after the cooldown of the weapon is longer than the under-fire timeout.(cheap and easily circumventable, but I have no better idea)
Another way would be to increase the percentage of the under-fire shield-regeneration, so the player, who was shot at first, hasn't lost from the first "turn".