Natural is not a coherent concept.
Paedophilia is bad because if indulged in, it would almost certainly cause severe life-long psychological harm to the survivor because they are not mature enough to deal with sex emotionally, and because they're innocent and not fully developed emotionally and cognitively, they are unable to give informed consent. Incidentally, most people who abuse children sexually are not paedophiles and many paedophiles don't act on their drives. You need to have a problem with impulse control as well for it to be a problem.
Homosexual relationships are ideally between consenting adults. They're not similar to paedophilia at all. If there's no consent then it's rape and obviously as wrong as heterosexual rape.
One way of defining mental illness is to determine if it's a danger to self and/or others. Paedophilia, if acted upon, clearly is a danger to others, i.e. the victims. Homosexuality, if acted upon, is right or wrong in the same circumstances to heterosexuality.