Honestly, this isn't the first time this has happened. Back in chapter 10, when he threatened her family, he was made to bow his head and apologize.
He apologized, and it never happened again in front of her. But to find out that he's still talking like that behind her back, it also makes it seem like the Emperor only forced the apology for show, and accepts that behavior in private.
Sidis' feelings are probably being misunderstood, but it seems that she's absolutely not mistake about the danger she's in by revealing her past. Her being experimented on seems to be a real issue, and they are hiding things from her.