Don't forget that Ico didn't exactly tilt his jar, the vibrations from the floor moving jostled it along with the fact that the ground it was on was already crumbling away.
She didn't just kill them because that probably means she couldn't use them as her shadowy soldiers. Or she needed them specially processed in those tombs for some reason. She probably wasn't just asking for horned kids just For the Evulz.
The book's explanation is that they were placed in the sarcophagi by the neighbouring Holy Zagrenda-Sol Empire so that they would protect Yorda and force her to continue freezing the castle in time, so the Queen would never leave the castle again. The Queen had nothing to do with it.
Ignoring the book, look what happens when the Queen is killed: the sarcophagi suddenly all activate simultaneously and zap Yorda with a bunch of energy, undoing the petrification (and turning her into a shadow, apparently temporarily). Further, they seem to contain the souls of the horned sacrifices when Ico revisits the room. Possibly those sarcophagi act as containers for life force or something, and would have fueled the Queen's Body Surf to Yorda's body.
One thing I am curious about is how did Ico wind up on that hanging cage after being dropped from the bridge? Unless he somehow had a forward momentum as he fell (and the scene gives no such indication), it's almost like an act of god that he miraculously didn't hit the water below and die. Of course, it's also baffling to think he may have fallen on the cage, and yet didn't break every bone in his body.
You guys are thinking of the wrong scene. The OP isn't talking about her sticking him in the cage at the start, the OP is talking about when he falls on top of the cage after the bridge scene, when Yorda's captured.
The same reason that Ico doesn't keel over from starvation/fatigue during middle third of the game — the curse of Dormin protects him from dying somehow.