The sentence: 'She didn't, truly, do anything wrong' means that it is true to say that she did not do anything wrong; the sentence: 'She, truly, didn't do anything wrong' refers specifically to 'she' and the implication is that while others may have done something wrong, she did not. The difference in meaning is very slight; there is only a slight difference in emphasis.

The commas are not incorrect, but they're unnecessary, and you should leave them out (unless perhaps you're writing a dialogue and you really want the reader to hear that there is a strong pause between the words). The form "didn't truly do" uses "truly" in a literal way, where it means "actually" or "in truth." For example, "I told him that I cleaned my room, but I didn't truly do it." You told him something, but it was not true -- you didn't "truly" or "actually" do what you said. The structure "truly didn't do" can also be taken literally (with the same meaning as above), but it can also be seen as simply using the word "truly" for emphasis. "I didn't do it" has a more neutral tone, but "I truly didn't do it" is stronger. You are emphasizing that you didn't do it. You could replace the word "truly" with "sincerely" or "really" or "absolutely." Shirley is also correct that, if you do use the commas in the form "she, truly, didn't," then the implication is that the word "truly" refers specifically to the subject, "she," emphasizing that SHE personally did nothing wrong.

That sounds odd to me. I would write: She truly didn't do anything wrong. without commas in this case