I'm of the opinion Kubrick changed the story so that in the movie, Alex was faking that the conditioning worked.
Basically I was convinced by the case made by this analysis from a guy named Rob Ager. Here's a key excerpt:
In the book Alex spouts his own objection as the preacher and Minister
debate the morality of the Ludovico technique, “Me, me, me. How about
me? Where do I come into all this? Am I just like some animal or dog?
… Am I just to be like a clockwork orange?” The last line in
particular is crucial to the book’s themes, but Kubrick omitted it
entirely. In Kubrick’s rewrite Alex fakes his sickness response, burps
as he sits up (which he can do at will, as demonstrated during the
police interrogation scene) then asks “Was it alright? Did I do well
sir?” He knew perfectly well what was expected of him and he acted his
This indirect mutual agreement between Alex and the Minister was also
communicated through a short verbal interraction in the prison
courtyard. In the book Alex objects to the minister's statements and
is in turn chosen for the Ludovico treatment. Kubrick drastically
alters this interraction by having Alex lie that he was imprisoned for
"the accidental killing of a person". The Minister is impressed with
his ability to lie outright and responds "Excellent. He's
enterprising, aggressive, outgoing, young, bold, viscious. He'll do."
Why would the Minister need a criminal who is "enterprising"? Because
Alex is the type of lying opportunist who will pretend to go along
with the Ludovico program, which will mutually benefit the Minister's
aim of clearing out prisons to make space for political offenders.
Cutting down crime is merely an illusion he needs to fabricate to
justify this policy and Ludovico is the propaganda tool he needs. Alex
then responds by thanking the Minister for choosing him (this didn't
happen in the book). The Minister responds "Let's hope you make the
most of it my boy." He's basically telling Alex to put on the best act
he can for the doctors and the press.
Once released Alex finds that his old, comfortable life is no longer
available to him. In his parents’ flat he is unphased by the erotic
female portraits on the walls - shouldn't he be feeling ill as he did
with the woman on the stage? And he gives away his unchanged
aggression by swinging a fake punch near his father’s face, “Keeping
fit?” he asks. Where is his Ludovico aversion to violent impulse?