I think that this is an historic problem.
When Turkey was perceived as a very cheap destination twenty to thirty years ago, the initial package holidays were also sold as ''very cheap''. To keep them as cheap as possible the flights were at the low cost slots for take offs and landings, normally night or very early in the morning. This has simply followed on to the present day with the charter flights.
If you look at some of the schedule flights they are at more reasonable times.
The other thing is, if you are staying in a Hotel, leaving later in the day means that you would arrive fairly late at your resort, especially with the two hour time difference. The same applies to departing as the Hotels need to clean the rooms etc., but you obviously gain the two hours returning home.