I always loved how Besson handled that, it could've been disgusting or disturbing very easily, but in the end he plays the sexual tension just on the surface, while it's pretty clear that none of the characters really wanted any sexual interaction with each other; both of them were oblivious to tender human relationships and, since Mathilda is a "grown too fast kid" going through early puberty, she probably interprets it as sexual love, while it's not (she even says as much when talking about a weight in her stomach going away).
Leon on the other hand never expresses as much, and is just generally awkward because he has encountered another human being that cares for him (him being a never grown up adult, emotionally retarded at times, also a serial murderer).
It's a weird relationship no doubt, but it's never in bad taste imo, the way they shift from mother/son (when Mathilda teaches Leon to read, or does the chores for him or teaches him to sleep in a bed) to Father/daughter (when Leon is being protective and taking care of her, especially at the end when Mathilda is freaking out) is at the core.
I think the lovers angle is played just on the surface and it's just Mathilda being confused as how to interpret this father/son figure, while also going through hormonal changes, coupled with her need to get attention (with the hotel receptionist or at the restoraunt, for example).
