I am not so sure that it is the case that OT narratives were allegorised, as if the historical context were ignored. Rather the Fathers interpreted the Scriptures on a variety of levels.
So the account of Jonah and the Big Fish was understood to have happened in a particular time and place, and the narrative provided evidence of God's concern for the Ninevites, the demands on Jonah of obedience, the possibility of Jonah having a second chance etc. But it also provided what was considered a type of Christ, and there is a clear understanding in the Fathers that there is a level of Christ-content throughout the Old Testament. But there is also a spiritual interpretation, and so when preaching one of the Fathers, and a priest today of course, will ask how the narrative impacts us. On this level the narrative will be detached from the historical context and used as a means of reflection based on the wider content of the Christian message.
So I understand the Fathers to use all of these levels. I don't sense that they deny or diminish the historical context. But they place these interpretations in a hierarchy of spiritual value. They might well say - it is interesting to read about how Jonah tried to run away from God, but what is more important is the lesson we learn about ..... whatever. The Bible is, in one sense, not about Jonah, but it is always about God and the salvation of mankind, and especially the salvation of the soul reading or hearing the Scriptures. As Gebre has said, the Scriptures are rooted in history, but their meaning and value is not limited to history.