You know her falling in love with him is quite plausible in that situation. He's the first adult ever to be nice to her. I give kudos to Besson for having Leon keep it a father/daughter, mentor/student, friend relationship. If you watch the version with deleted scenes, he refuses her advances.
Of course what disturbed most people was a 12 year-old girl learning to become an assassin, and taking part in hits.
Your point about her being naturally attracted to the only adult male that had ever paid attention to her is true, but this is also problematic. The assassin, as depicted, would probably have had a sex drive, but like other people of low intelligence, would not channel or control that drive, and would likely respond positively to her advances. I would submit that the reason he spurned her advances was not an artistic decision, but a marketing decision to allow the movie mass distribution, as opposed to the minuscule distribution that a movie like "Hound Dog" received. The Professional played to the pedophile angle while staying far enough within the norms to avoid censorship.
A lot of men are attracted to underage girls. This is the reason so many men from all walks of life are arrested for child pornography and attempting to meet underage girls on the internet. Jon Benet Ramsey became a big story because stories about her drew ratings. Stories about her drew ratings because there were photos of a five year old girl dressed up like a Las Vegas showgirl. If Jon Benet Ramsey had been ugly, there would have been no stories, other than a write up locally.