I bet the emperor always planned to cover up the mother's crimes, since pursuing it would make Philomel the daughter of a criminal, and thus unsuitable to stay in the royal family no matter what the emperor said. I am curious as to why he kept asking elincia if she was sure though; maybe he wanted to cover up the crime, but it would only work if elincia, the main 'victim', chose not to press charges? It would be nice if we could see a bit more into his thoughts.
Also, why is baby philomel so heartbreakingly cute? Just the image of tiny her politely asking the priest if she got her name in is almost too much! It's a wonder how everybody was able to be cold to her with that adorable face