A History of the Fortress
A new subtext emerges from the story of Ico if we combine this analysis of the roles of the Ancients and the people with horns, the burden the latter carry until Ico's actions lift it, and the minor but significant observation that Yorda seems to have a particular title for Ico despite not knowing who exactly he is.
From the historical perspective of the Ancients, the people with horns have an aspect of something unwanted and possibly threatening about them. While it is not their own fault, they must nonetheless be dealt with on those terms. This would of course cause such people to be seen and treated badly, just as Ico's village saw him as a curse and sacrificed him. The end result of this would be that sacrificing, or otherwise dealing with, anyone with horns would go from an unfortunate necessity to a matter-of-course punishment them for a crime they did not commit.
Keeping that thought in mind, lets look at where the individuals Ico and Yorda come into this. From this historical perspective, of which neither of them are aware, they are on the opposite sides of this divide. Due to Yorda being a Light Being, and Ico inheriting this association with Dark Magic, they should be enemies. But, due to being ignorant of this history, they are not. The one thing which hints at this history is the title Yorda gives Ico, which is 'Ico'. As I mention in the character analysis of Ico, this must be a title rather than a name, and likely refers to what he is rather than who he is - and what he is is a person with horns. Yorda unwittingly references this historic conflict, setting the stage for its final chapter.
The power which the people with horns were sacrificed to contain ended up taking over the Fortress. The Queen's selfish turn to the opposing side and the abandonment of the Fortress to the Spirits was effectively a victory for the power the Ancients, Yorda's people, opposed. And now another more powerful Dark Being is going to be responsible for yet more harm against the living - the Queen intends to kill Yorda, and whats more her plan will use the power the people with horns hold.
At least in this one possible subtext.
Written by Crumplecorn