First, observe the rule for the sequence of tenses: 1. He was molested -- 2. It took me some time to accept. -- It took me some time to accept that he had been molested.
Secondly, deal with at first. The way it is written renders the sentence illogical:
At first, I simply couldn't accept the fact that he had been molested.
Not everything which seems clear is grammatically justified, my friend. There should be an antedote to the doctrine that whatever emerges from people’s lips is the language and that many verbal wrongs make a right. Using perfect past is preferable to not using it in the present instance.
The house had been painted/was painted yellow before they changed it to pink. Often using the past tense instead of the past perfect tense is acceptable.
Sorry, but the clippings you pasted from the web-site (as reputable as it may be) does not bear on the subject discussed. Please revise what the rule for the sequence of tenses refers to and in what instances it should be applied without any digressions. A final remark: when grammarians (or would-be grammarians) utter something like: 'Often using the past tense instead of th