Oracle: Our time is up. Listen to me, Neo. You can save Zion if you reach The Source, but to do that you will need the Keymaker.
Neo: The Keymaker?
Oracle: Yes, he disappeared some time ago. We did not know what happened to him until now. He's being held prisoner by a very dangerous program, one of the oldest of us. He is called the Merovingian, and he will not let him go willingly.

Referring to the bolded statement above, how in the world could the Oracle not know what happened to the Keymaker until recently? She can see all things happening in the Matrix, so why not this? And since the Keymaker is a program in the Matrix, there is absolutely no way the Merovingian could successfully kidnap the Keymaker without the Oracle knowing before it happens. What this means is that the Merovingian did not kidnap the Keymaker. In ETM, the Keymaker says he is "held captive" and "imprisoned" by the Merovingian, but he never says he was kidnapped.

The beauty of a good theory is that the puzzle pieces fall into place when they are arranged accordingly. Allow me to arrange the pieces so you can try to put them together yourself:

In other words, I think the Keymaker was busy working on something inside of the Source (perhaps the gateway Neo takes to the Source), which would be a place that lies outside of the Oracle's vision. If the system (i.e. the Architect) had decided to delete the Keymaker at that instant, the Oracle wouldn't have been aware of it. The Keymaker would have been flagged for deletion by the system (a decision that would have been made outside of the Matrix system, perhaps by the Architect), and the Keymaker would have chosen exile of course, since he still feels able to fulfill his purpose.

Why was the Keymaker flagged for deletion?

When Smith first gained access to the backdoors, that is probably when the Keymaker lost his purpose. Since Smith had all the keys to the backdoors, the system needed to "change the locks" of the doors, which unfortunately also meant changing (or at least upgrading) the locksmith. The Keymaker is still doing what he was originally programmed to do, which does not take into account the Smith "security breach". The system needed to upgrade the Keymaker in order to ensure that Neo could reach the Source. By calling for deletion of the Keymaker, the system was actually trying to protect Neo even though it appears at first that the system is trying to get in Neo's way.

The Oracle could not see this coming since decisions for deleting and upgrading programs are made by the Architect, who does not reside in the Matrix.

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