Naruto decided on running away was the best course of action. And it was.
So he made a plan. And the priest would help.
You see, the priest had never actually molested Naruto. It was all a trick. He pretended to violate Naruto in the most hurtful of ways in order to help Naruto get way from his parents. It was the perfect secret plan with no flaws.
The priest would pretend to hold Naruto captive in his torture sex dungeon so his parents wouldn't look for him while Naruto escaped and (insert plot device). This would buy him potentially weeks worth of head start before they realized something was off.
And the plan worked! My god, the plan was so vague and convoluted Naruto wasn't sure if it would pan out. In the end though, his fears were for nothing.
A month passed and his parents started to get worried. What if the priest had accidentally raped their son to death thereby releasing him of his worldly suffering? That just wouldn't do.
So they went to check on him on him. They found out the priest had lied and protected their son. They killed him for not molesting their son.
Then another month of searching passed and slowly realized they loved their son. When they denied him food and tortured him and kicked him in the balls, it was out of love not hate! How could they have been so blind?
So when the found Naruto they doubled up on the neglect and abuse and made sure to leave Naruto with a registered sex offender on a frequent basis.
Out of love of course.