It's disturbingly easy to rewrite a reploid's free will. You must have noticed that yourself when Weil came into power. I would not have imagined that a human could be "reprogrammed" as easily as a reploid, but if they bent you to their will so completely, it's entirely possible that they have altered Ciel to suit their own purposes as well.

[Pen taps. Just one or two of them.] As for you... whether or not you were reprogrammed, you turned your weapon on Master X. Even if you didn't believe he was X, then from that point of view, you attacked a human that was already injured. Whatever changes were made to your programming may lie dormant within you still. That's not something I can take lightly.