Actually, Tom Riddle IS evil, before he went to Hogwarts he started using his magic to control, steal things, basically terrorizing other kids that were in the orphanage with him for god's sake. He researched the Chamber of Secrets for 5 years before he realeased it...
tl:dr - Tom Riddle was one fucked up evil kid.
And molesting him to wake him up? What. The. Fuck?