Well, it depends on your interpretation of the phrase "buy Academic Knowledge skills at half price (round up)" and in particular how you determine when to "round up."
Chummer is handling it by rounding the skills individually, and based on your question you thought it would be done for all of the academic skills as a whole.
I'm not sure which method is "correct," but Chummer's method is probably the safer bet especially for programming. It is a lot easier to have the program go through all of the academic knowledge skills and halve the cost being applied by them, rounding up. Trying to give a discount based on all of the skills overall would involve applying a discount to half of the skills and would be mildly confusing at best if the user isn't paying close attention...
So, to answer your question: Yes, Chummer is applying the effects of the quality in a correct way. You might be able to argue with a GM to allow you to take 10 rank 1 knowledge skills for the price of five, but it isn't explicitly worded that way. Technically by a strict reading of the quality you would look at each skill individually, and halve the costs for it at character creation (rounding up).
Side Note: since the other part of the quality (post character creation) explicitly gives a bonus on skills only of rank 3+, I would also argue that the quality is meant to allow you to take several skills at higher ranks for less cost rather than tons of super low rank skills.