I think y'all are underestimating Onee-san.
She has her own affection towards him, she might not fully understand it yet, but she definitely likes him. She's got a good head on her shoulders, but she's also free-spirited. She's not the MOST responsible adult, but she doesn't overtly try to cause problems at her workplace. She's a lot like the FMC from Gal Gohan. She's hiding her affection of Shounen behind teasing.
And everybody knows that the endgame of "liking someone" is getting them to like you back, so she's in it to win it.