Denise,
Yes, you can request certain carriers if you're using RSSC air. If you don't get what you like you can select custom air through them and pay the $100 fee. As you're staying in Istanbul for a post cruise you'd pay the deviation fee anyway.
The time of year you're going the flights are not badly priced. Unless you're using mileage to fly business, I'd just pay for the flight. I just looked at Orbitz and you could fly Lufthansa LAX leaving at 2:55 pm arriving FRA 10:25 am, connecting (on LH) to Athens leaving at 1pm arriving 4:45pm. The return is out of IST at 8:05 am to Munich arriving 9:35 am connecting on LH 11:10 arriving LAX at 2:25 pm. The price is running about $1173 RT. You'd have to pay for a hotel for 1 night in Athens, but you wouldn't have those horrible layovers and would be fresh for the cruise! What are you going to do in Athens between 4am and the time you board?? Just an idea...and you'd get about 13,000 miles!