Of the champions that take Conqueror, Darius is the only one that deals damage over time. And there's a penalty in place for DoT to prevent him and him alone from fully stacking it in two seconds.
So why is it hard to understand the fact that other abilities that can hit multiple times in short succession, similar to DoT, are an issue with the current functionality of the rune? It isn't that the champions are overpowered. It's that there was no similar penalty put in place to stop them from doing exactly what DoT would do without the mechanical penalty.
If, like DoT, the same ability could only stack/extend Conqueror once every 5s, champions who hit with the same ability multiple times within 5s wouldn't be able to fully stack it twice as fast as other users.
And just like how the DoT penalty has no effect whatsoever on champions who don't have DoT, this wouldn't effect champions who don't have multi-hit abilities. They'd still be able to stack it completely normally with their abilities and auto attacks. (If it's unclear, my suggestion only applies to abilities. Autos would still be able to stack/extend it every hit)