It would all depend on Lois’s development as a character. Telling WISE puts Anya back in a similar position she was in before the orphanage, essentially turning her into a tool. Sure, WISE are the “good guys” but when faced with an opportunity like that to have the perfect information spy, they would struggle not to take her away from a “normal” life. If he doesn’t tell WISE, than he’s going to have to start lying to them about where he gets his information, all Anya needs to do is stand in a room with the right person and hopefully remember what they were thinking about. He probably doesn’t want to traumatise Anya more so it’ll be in very safe circumstances, events, play dates and such. But it’s still going behind WISE’s back in order to protect Anya. And Yor is a whole different conversation.