The main point I think is that Sakura wouldn't feel that way if Medusa wasn't creepin'. I know its annoying when you want to see a ship you like, but its just the truth of the matter based on that context. There is an negative air between the two primarily because Medusa is the one being dishonest(she bribes both Sakura and Shirou because she knows she is working under the table so to speak), otherwise it would be fine.
Though I will admit that the book scene is trying to play the jealousy comedy trope too hard. But its few and far between when its layer on that thick.
Heck we even have a scene where Sakura tells Shirou to essentially take Medusa out on the town while she takes care of her injured kouhai. Plenty of other examples like that. Plus I remember saying before all the heroines have instances of being catty with each other about Shirou. Sakura mainly seems like the most noticeable because she has stigma.