Midgardsormr didn't just let them out. He was Keeper of the Lake for a reason. He was guarding the seal that was in Mor Dhona because of the aether. Once his battle with the Garleans was under way and he died along with destroying that great big battle ship the explosion broke that seal. So it was all by accident. With all that aether available it allowed Eorzea's beast tribes to summon the primals because of all the excess aether bubbling about.