Pixel, it is specifically mentioned in the "Creating a Shapeshifter" section on page 102 of Run Faster that the Negative Quality can be bought off with Karma. It simply specifies that a good reason is needed. In reference to Uneducated, you need a good reason why the shifter has been properly educated.
As for the cost, the only other instance of negative qualities needing to be bought off during chargen would be the Life Modules creation system. Normally, if you don't want a negative quality you simply wouldn't pick it, but like some racial-tied negatives, life modules can also apply negative qualities that you may want to remove before finishing up your character. Likewise, the life modules rules don't mention the cost being doubled at this step.
My opinion would be that since the character is not yet finished, the advancements costs don't apply. The cost to remove a Negative quality being valued at "Bonus Karma Value x2" is part of the character advancement rules. During creation qualities all just have values which are freely exchanged to and fro with karma, no need to double anything until after the creation stage is finished.