I'm not understanding why you think classifying pedophilia as a mental illness is apologetic. It doesn't make the crime any less wrong. In fact, it's what makes a pedophile one of the most dangerous offenders out there--the fact that it is a mental illness makes them more likely to repeat their offense, if they've acted on their urges, which was my original point.
Pedophilia was indeed wide-spread in ancient Rome and Greece, but now you're entering into cultural psychology, which is not applicable in this case. Roman Polanski did not grow up in ancient Rome or ancient Greece. He grew up in modern Western culture, which strongly emphasizes early on that children are children, and they are not to be sexualized. Other cultures are not so firm on this, but Western culture is. He committed his crime in the United States, which takes a firm stance on not engaging in sexual behavior with children.
There are several symptoms you can identify in a sociopath who hasn't committed an offense, just as there are plenty of symptoms you can identify in a pedophile, even if they haven't abused anyone. One is isolation--pedophiles often feel that they can't relate to people their own age. Another is good interpersonal skills only with children. Pedophiles, like sociopaths, tend to be very attractive to their victims.
Probably the most obvious symptom of pedophilia is having intense, consistent fantasies involving a prepubescent child, usually about thirteen years old or younger. Usually, they last about six months, and either cause clinically significant distress/social impairment, or the phenomenon of rationalization, which makes it even more dangerous.
There are also plenty of identifiable symptoms of sociopathism which can be caught before the person has committed an offense, but we're not talking about sociopaths, so I won't list them. You said that "being a paodophile makes you a callous, calculating individual with a need for power over their victims, with a choice over right and wrong," and that is true. A pedophile is a sick individual. This does not mean sick in the sense that one is deserving of pity, but it does make them very dangerous, because nothing really cures pedophilia except prevention. Once the crime has been committed, the individual is highly likely to commit it again.
Alcoholism, drug addiction and depression are inarguably illnesses. That doesn't mean that there are no bad choices involved, but you can have an addictive personality, which makes you more likely to develop the disease. And I'm sorry, but I'm actually pretty offended by what you have to say about depression--so someone who is depressed isn't "very nice" and has made "bad choices?"?
You can actually see all of these mental illnesses on the brain. Certain things go on chemically, which we can't help. There is, of course, always an aspect of it that involves an individual's decision-making and character (which, by the way, is part of psychology), but that's only half of the picture.
You said that "there are times when medical science and psychology should butt out and realise that sometimes people aren't very nice and they make bad choices," but science and realizing that "sometimes people aren't very nice and they make bad choices" aren't mutually exclusive. The bottom line is, referring to pedophilia as an illness is a fact, and that doesn't make the crime any less awful. If anything, it gives it even more of an edge because, as I said, it makes it more likely that they will act again.