Along with such terms as sadism, masochism, homosexual, bisexual, and gerontophilia, the word pedophilia first appeared in Richard von Krafft-Ebing's pioneering work on the psychology of human sexuality, Psychopathia Sexualis, first published in 1896.
Krafft-Ebing not only chose to title his book in Latin, but also composed more sensitive passages in that language so that discussions of the topic would remain among educated elites, all of whom would have studied Latin and Ancient Greek. In that sense, the word is more academic jargon than strictly speaking a euphemism. Since Krafft-Ebing, like the Greek Stoics before him, believed that any sexual activity outside of procreation was somehow pathological, then the term pedophilia was definitely not coined by an apologist. The Greek term, however, might still be considered a euphemism compared to the German Knabenschänder ‘defiler of boys’ first attested in Martin Luther’s translation of 1 Cor 6.9.
In using the component -philia or -phile to denote sexual excitement or desire directed toward the first part of the compound, Krafft-Ebing follows the lead of the French Belgian psychologist Joseph Guislain, who coined the term necrophilia around 1850 to describe the desecration of corpses for sexual gratification by François Bertrand, a soldier in the French army.
This time, however, the term quickly escaped the academy as Bertrand was reviled in the popular press as le Sergent nécrophile or le Vampire de Montparnasse [Cemetery].
The pattern set by Guislain and Krafft-Ebing remained productive throughout the twentieth century. The Dutch psychologist Frits Bernard, for instance, further refined the concept of pedophilia by coining the term ephebophilia in 1950 to describe an adult sexual attraction to mid- to late adolescents.
Why not Eros?
Modern words crafted from ancient languages are coined to fill a modern need, not to imitate the thought word of the ancients. Neither French, German, nor English preserves the distinction between erotic Eros and the non-erotic Philos, so native speakers of those languages likely feel not great urge to distinguish them either, especially in compound words. And while erato- can function as a prefix, as in eratomania, another modern coinage, I'm not sure how that word could function as the second element of a compound noun. The suffix -phile or -phil, however, had already entered those languages meaning ‘a lover of’, so -philia seemed like a ready solution. Besides, once Guislain or some scholar before him defined -philia to mean sexual attraction/gratification, it was available to his learned colleagues regardless of what long dead Greeks or Romans might have thought of the coinage.