You're very close to right.
After shooting Ms. Freeman with a shotgun, Mr. Tharpe kidnapped his wife and allegedly sexually assaulted her.
In this sentence, the shooting and the kidnapping are presented as facts. In contrast, the sexual assault is presented as an allegation. That is to say, the adverb "allegedly" does not apply to the entire sentence, but it does apply to the entire predicate "sexually assaulted her".
You've paraphrased this sentence as follows:
After shooting Ms. Freeman with a shotgun, Mr. Tharpe kidnapped his wife and, allegedly, he assaulted her sexually.
Given this structure, "allegedly" applies to the entire clause "he assaulted her sexually". It still doesn't apply to the entire sentence, and the shooting and kidnapping are still presented as facts rather than allegations.
You seem to understand the semantics of the original sentence correctly, and you have paraphrased that sentence successfully. Your mistake lies in confusing a sentence with the constituents that the sentence contains.
That is an important distinction to make.