They didn't do anything sexual until the alpha turned 18 and the omega didn't fantasize about having sex with the child alpha. BUT because it is omegaverse and they were fated pairs the omega was instinctively drawn to his mate's side. He nearly OD'd on suppressants so he would not go into heat nor make the alpha go into rut prematurely. I don't see that as pedophilia. Imho I thought this was a fluffy story.
Shingeki no Kyojin dj - Ore no Alpha