The whole point of ranged combat is to effect the other player before he can affect you, and move away before he reaches you. This is fundamentally what ranged classes do. Be it on a roof, behind a barrel, tree or whatever cover they can find.
I think this is the central statement in your post. And basically you are right here.
But what you brought up as an argument for your position is actually my argument for mine:
While you are enabling one class to effectively engage the other (melee versus ranged), your are disabling the other one from effectively doing the same (ranged versus melee in this case), this is not really a solution, just shifting the "problem" (I'm still not convinced there is a problem) somewhere else.
In least cases balancing is about clear, absolute facts. Usually it's more about subjective feelings and preferences.
In my opinion Warband Native has a very good balance. So it could serve as basic point of orientation.
In Native there are no ladders, and yet the archers do fine. So in my opinion, the ladders shifted already the balance to their favour, and so I think removing ladders would more or less "fix" this issue.
Let me say it this way:
Chances of infantry and cavalry getting up on a rooftop full of archers over a (breakable!) ladder without dying are way worse than chances of archers on the ground trying to successfully keep distance to melee fighters using his higher mobility by higher agility values and less encumbrance (and, not to forget, teammates and cover/obstacles on the ground).
Or, even easier:
Archers on rooftop vs. infantry on ground is no fair battle
Archers on rooftop vs. cavalry on ground is no fair battle
Archers on rooftop vs. archers on ground is fair battle
The rock-paper-cissors-system actually DOES require you to have two unfair battles, BUT one of it should be to your disadvantage, and not both favouring you heavily.
Bottom line: introducing ladders moved balance heavily to the favour of the archers. This needs to be fixed. I am already content with server rules forbidding to shoot from a roof without access at ANY TIME of the battle.