I think the comments cover Besson's personal issues thoroughly so I won't reiterate, but will assume the reader is aware.

It's also been noted here that there are multiple versions: Leon (International), The Professional (American), and Leon: The Professional (Extended/DVD). And I think each is defensible as the 'definitive' version but I tend to prefer the Extended because the severity of it has an added value. There's no mistaking it for revenge fantasy.

For the purpose of comparison, consider Hit Girl avenging Big Daddy in Kick Ass. She is far more active in the violence than Mathilde is every version of Leon combined*.* Yet that movie is able to treat it as fantasy, escapist. Not to knock it, the bad guys get what they deserve and it's fun. But, I've never thought that's what Besson was after and I tend to think the international and extended editions emphasize that intention more than the American.

I think you'd be more forgiven for watching the American version and thinking "the paedo is trying to get away with something." But the more salacious cuts have a way of implicating the audience more than the author. That the camera treats her like an adult emphasizes how she's been robbed of innocence. We can see the vast disparity between how she sees herself and how we see her.

So while I understand why and how people are uncomfortable, I believe that discomfort was always the intention and have never really thought that Besson was broadcasting his own preferences--so to speak.