Well, certainly the Church would teach Pharaoh was not tortured underwater for 50 days without dying.
Now, unless the Talmud is trying to make the point (in an odd way based on your description) that the King of Nineveh was a type of Pharaoh (or, rather, Pharaoh was a type of the King?), and that evil has always survived, or something along those lines, then this is ample evidence of the vast difference in the Jews of the Old Testament and those of today (not, of course, in their ethnic heritage, though many Jews today are undoubtedly descendants of the many, many converts to Judaism during the Roman Empire's time), and how Judaism has not remained unchanged, even during the Temple period.
The story in the Jewish Legend did not say that the King of Nineveh was a type of Pharaoh. The person recording the story did not intend to make an allegorical association between Pharaoh and the King of Nineveh. He wrote that Pharaoh was the same person as the King of Nineveh. The reason for this claim was the significance of repentance attached to Pharaoh's supposed conversion in the same legend. The Talmud says repentance is so significant that Elohim forgave even the repentant Pharaoh. The King of Nineveh repented as soon as he heard Jonah's preaching because as the Pharaoh of the Exodus, he was already familiar with God's mercy to repenting sinners.
I personally think that the assertion concerning Pharaoh's survival in the Jewish Legend may have originated from the ambiguous nature of the Biblical narrative in the Book of Exodus. There is actually no Bible verse that explicitly says the Pharaoh drowned with his army.