Theres an inyan to make a bracha on a dvar shalem: On an whole fruit. If someone likes to eat an apple pealed, should he first make a bracha on the apple unpeeled, take a bite and then peel it, or is it better to peel it and then make a bracha? It might be different with an orange which is never eaten unpeeled. Which is the greater shevach to Hashem?
This would ostensibly be a question of chaviv against shalem: the peeled apple is chaviv, but not shalem. If so, the shalem would come first (see Shulchan Aruch 211:1-2, and Mishnah Berurah 211:4).
However, the order of preference applies when a person has a choice of two fruits, both of which he desires to eat. In this case, one desires to eat only the peeled apple, and one does not wish to eat the apple without peeling it. Therefore, it appears that in this case, the ‘order’ would not apply, because there is no ‘order.’ There would thus be no obligation to make the berachah on the apple before peeling it, and it would seem preferable to peel the apple before making the berachah, because making a berahchah on something one doesn’t want to eat may be a certain flaw in the berachah.
In addition, according to Rambam chaviv comes before shalem (another reason to peel before making the berachah).