Try to find a vector which incorporates its DNA only in mitochondrial DNA. That's the way that plant genetic engineering has started up by the way (with a bacterial vector in that case). Maybe some virus can be found which inserts its DNA in mitochondria only?
I figger ther is not much else one can do. No?
Why do I make that suggestion? Well there is a theory with stands pretty strong stating that mitochondria are sort of originating from symbiotic bacteria in eukaryotic cells. Maybe there are virusses which are still able to infect the mitochondrion from the time it was a symbiotic bacterium.
Maybe it's looking for a needle in a haystack, but if you find such a virus, you have your vector and secondly you will be close to a Noble price.