It seems to me that if the Go'el ha'Dam kills the Rotze'ach when he is in the airspace above the Ir Miklat, the Goel ha'Dam would not be put to death.

This is because the Gemara states (three lines from the bottom of 12a) that concerning Ir Miklat it all depends on "Dirah" -- where one resides. Even though the root of the tree is inside the city of refuge, since the spreading leaves of the tree are outside the city, we say that the Rotze'ach is not considered as being inside the Ir Miklat, because under the leaves is a more suitable place for living than the roots of the tree.

Similarly, we can say that "up in the air" is not a place where one can live, so the Rotze'ach is not considered to be inside the city. (See also Ayeles ha'Shachar.)

Kol Tuv,

Dovid Bloom