Why was Jonah allowed to disobey?

Closeup of Michelangelo's The Prophet Jonah,
From Wikipedia

Jonah 1:1-4  Now the word of the LORD came unto Jonah the son of Amittai, saying,  (2)  Arise, go to Nineveh, that great city, and cry against it; for their wickedness is come up before me.  (3)  But Jonah rose up to flee unto Tarshish from the presence of the LORD, and went down to Joppa; and he found a ship going to Tarshish: so he paid the fare thereof, and went down into it, to go with them unto Tarshish from the presence of the LORD.  (4)  But the LORD sent out a great wind into the sea, and there was a mighty tempest in the sea, so that the ship was like to be broken.

God commanded Jonah to go to Nineveh and Jonah said "no". I read the third verse almost wincing as you see the disobedient servant walk away from the direct and clear Word of God straight into rebellion. It is sad to see one throw up his hands and walk away from the presence of the Lord. But why would God allow Jonah to do this?

One reason is that God would be glorified. The sailors praised God in the storm later in the chapter. Jonah praised God in his prayer and Nineveh feared God when Jonah came to town, no doubt hearing of what happened. Jonah made a splash when he was tossed in the sea, the ripples of which are still felt these centuries later. The experiences in the Old Testament happened for our examples (1Co 10:6). We need to read of Jonah and be warned. God allowed Jonah to disobey so we will learn no to.

It was also for Jonah's own good in his own spiritual walk. Hugh Martin says:

"Jonah may not, indeed, be strong enough yet for thus prosecuting fearlessly the work given him to do  He may not yet set himself so simply, so fully in the word and wisdom of the Lord as to silence and crucify the wisdom of his own carnal reason -- the light of the Lord not yet being allowed calmly and alone to shine upon his heart and indicate his path. He may need to be brought through a terrible experience of his own, before his faith be pure enough, before his shield and sword for such a warfare be wielded into sufficient tone and temper for securing him the victory. "judgment may begin" first on himself, in the appalling affliction that his waywardness brings upon him. But shall the Lord's quarrel with Nineveh therefore not be pleaded? Nay; it shall be pleased more emphatically by far on account of any such delay. Jonah shall come to them at last with all the unshrinking strenuousness and firm nerve of a man, who fresh from terrific trial, visible and invisible, feareth not the face of clay. The very presence of the man among them shall say "If judgment begin upon the prophet of the Lord, what shall the end be of them that obey not his word?" And when then he shall deliver Jehovah's word of judgment, as if his own soul were standing the gates of that eternal world from which he has been miraculously redeemed, and his eye filled with its tremendous revelations, there shall be a tone of unflinching certainty and majestic terror in his voice, worthy of the redeemed herald of the King of kings, infixing amazement and conviction into the hearts of his foes."

 Perhaps Jonah was not yet ready for the work that God had for him and he was not yet ready to bear the message. God had to tune the man for the message that He wanted delivered. It has been said that God draws straight lines with crooked sticks. Jonah meant his disobedience for evil and rebellion, God meant it to strengthen Jonah for future service. God had Jonah's good in mind because Romans 8:28 was true, even before it was written.