Alex and the droogs beat the piss out of a pyahnitsa ded, prevent a Devotchka from being raped by battling a rival gang, and then go on to rape a few cheenas themselves. Of course, bad deeds don't go unpaid, and Alex is turned upon by his shaika, and left hanging in the wind. He's left to reenter society half the man he was, and face the people he once maligned, who are now after him much the way he was after them. It's never really stated in the film - the film makes no sense of it, and it's such a visual term, that it's hard to apply common sense to it anyway. But look no further my brothers - the answer is simple, and very metaphorical.
Moral freedom is a human being's own choice to be able to perform both good and evil at any moment.
The important thing is moral choice. Evil has to exist along with good, in order that moral choice may operate. Of course, moral freedom is never truly attained in the film, because Alex is neither totally good, or totally evil, but a full mix of both characteristics. This holds true, even after the conditioning Alex goes through with the Government. It is true that the Government tries to make Alex totally good through conditioning, but because it's coerced goodness, moral freedom is not truly achieved.