There are bus services with several bus companies almost hourly throughout the day and evening for this 10 hour journey,cost 60TL.
To go Konya>Ankara>Malatya you need to first take the high speed train to Ankara which takes 2 hours ,cost 25TL economy class or 35TL business class.You'll need to be at the airport 1 hour before departure of a flight to Malatya.
The costs of flights vary but looking now for the coming month as an example,the only carrier going direct is Anadolujet,the budget arm of Turkish Airlines(others fly via Istanbul...hey ho!).Prices are coming up at 100-155TL for this 80 minute flight.Plus cost of transport to and from airports.
So basically flying is at least double the cost but almost half the time of the bus.BTW,if you take the overnight bus with Metro at 23.59 the journey only takes 8½ hours due to quieter roads.You'd save on a hotel bed cost that night too :)