I imagine this is because when the egg is fertalised the mitochondria in the sperm are discarded leaving only the maternal ones.
If you are asking why they don't extract the mitochondria from one of the fathers cells, extract the mitochondria from the egg and then implant the paternal mitochondria: I assume because that would be a lot more difficult and likely to damage/destroy the cells in question.
I am not a biologist so if any of this is wrong please someone correct me.
I am not a biologist either, but...
As far as I know, the difficulty lies in removing the faulty mitochondria while keeping the health nucleus in-place and undamaged. Its easier to remove the nucleus from the egg.
Mitochondria removal has been done with fertilised monkey eggs and unfertilised human aggs . The monkey eggs were implanted and produced apparently healthy animals. I guess the ethical problem with trying this with human embryos is the risk of unforseen effects.