She's the one who cooked the books from the get go. She went back to her old job and continued to cook the books so her boss and probably her wouldn't go to jail. Walt has his justifications too, but that doesn't make either moral.
she never cooked beneke's books in the first place. she used to work there, quit, the economy tanked, beneke messed with the accounting to stay afloat, she started working there again, saw inconsistencies, he admits to it, but she keeps doing it because she needs the money and she's banging ted.